Plants having enhanced yield-related traits and a method for making the same

ABSTRACT

The present invention relates generally to the field of molecular biology and concerns a method for enhancing yield-related traits in plants by modulating expression in a plant of a nucleic acid encoding an SGT1 polypeptide, or a CLC-pKG polypeptide, or a HD-hydrolase-like polypeptide. The present invention also concerns plants having modulated expression of a nucleic acid encoding an SGT1 polypeptide, or a CLC-pKG polypeptide, or a HD-hydrolase-like polypeptide, which plants have enhanced yield-related traits relative to corresponding wild type plants or other control plants. The invention also provides constructs useful in the methods of the invention.

RELATED APPLICATIONS

This application is a divisional application of U.S. application Ser.No. 13/498,003 filed Mar. 23, 2012, which is a national stageapplication (under 35 U.S.C. §371) of PCT/EP2010/064095, filed Sep. 24,2010 which claims benefit of European Application No. 09171385.9, filedSep. 25, 2009; European Application No. 09171364.4, filed Sep. 25, 2009;U.S. Provisional Application No. 61/252,220, filed Oct. 16, 2009; U.S.Provisional Application No. 61/252,215, filed Oct. 16, 2009; U.S.Provisional Application No. 61/260,942, filed Nov. 13, 2009; andEuropean Application No. 09175989.4, filed Nov. 13, 2009. The entirecontents of each of these applications are hereby incorporated byreference herein in their entirety.

SUBMISSION OF SEQUENCE LISTING

The Sequence Listing associated with this application is filed inelectronic format via EFS-Web and hereby incorporated by reference intothe specification in its entirety. The name of the text file containingthe Sequence Listing is Sequence_Listing_(—)074021_(—)0175_(—)01. Thesize of the text file is 627 KB and the text file was created on Sep. 3,2015.

The present invention relates generally to the field of molecularbiology and concerns a method for enhancing yield-related traits inplants by modulating expression in a plant of a nucleic acid encoding anSGT1 polypeptide, or a CLC-pKG polypeptide, or a HD-hydrolase-likepolypeptide. The present invention also concerns plants having modulatedexpression of a nucleic acid encoding an SGT1 polypeptide, or a CLC-pKGpolypeptide, or a HD-hydrolase-like polypeptide, which plants haveenhanced yield-related traits relative to corresponding wild type plantsor other control plants. The invention also provides constructs usefulin the methods of the invention.

The ever-increasing world population and the dwindling supply of arableland available for agriculture fuels research towards increasing theefficiency of agriculture. Conventional means for crop and horticulturalimprovements utilise selective breeding techniques to identify plantshaving desirable characteristics. However, such selective breedingtechniques have several drawbacks, namely that these techniques aretypically labour intensive and result in plants that often containheterogeneous genetic components that may not always result in thedesirable trait being passed on from parent plants. Advances inmolecular biology have allowed mankind to modify the germplasm ofanimals and plants. Genetic engineering of plants entails the isolationand manipulation of genetic material (typically in the form of DNA orRNA) and the subsequent introduction of that genetic material into aplant. Such technology has the capacity to deliver crops or plantshaving various improved economic, agronomic or horticultural traits.

A trait of particular economic interest is increased yield. Yield isnormally defined as the measurable produce of economic value from acrop. This may be defined in terms of quantity and/or quality. Yield isdirectly dependent on several factors, for example, the number and sizeof the organs, plant architecture (for example, the number of branches),seed production, leaf senescence and more. Root development, nutrientuptake, stress tolerance and early vigour may also be important factorsin determining yield. Optimizing the abovementioned factors maytherefore contribute to increasing crop yield.

Seed yield is a particularly important trait, since the seeds of manyplants are important for human and animal nutrition. Crops such as corn,rice, wheat, canola and soybean account for over half the total humancaloric intake, whether through direct consumption of the seedsthemselves or through consumption of meat products raised on processedseeds. They are also a source of sugars, oils and many kinds ofmetabolites used in industrial processes. Seeds contain an embryo (thesource of new shoots and roots) and an endosperm (the source ofnutrients for embryo growth during germination and during early growthof seedlings). The development of a seed involves many genes, andrequires the transfer of metabolites from the roots, leaves and stemsinto the growing seed. The endosperm, in particular, assimilates themetabolic precursors of carbohydrates, oils and proteins and synthesizesthem into storage macromolecules to fill out the grain.

Another important trait for many crops is early vigour. Improving earlyvigour is an important objective of modern rice breeding programs inboth temperate and tropical rice cultivars. Long roots are important forproper soil anchorage in water-seeded rice. Where rice is sown directlyinto flooded fields, and where plants must emerge rapidly through water,longer shoots are associated with vigour. Where drill-seeding ispracticed, longer mesocotyls and coleoptiles are important for goodseedling emergence. The ability to engineer early vigour into plantswould be of great importance in agriculture. For example, poor earlyvigour has been a limitation to the introduction of maize (Zea mays L.)hybrids based on Corn Belt germplasm in the European Atlantic.

A further important trait is that of improved abiotic stress tolerance.Abiotic stress is a primary cause of crop loss worldwide, reducingaverage yields for most major crop plants by more than 50% (Wang et al.,Planta 218, 1-14, 2003). Abiotic stresses may be caused by drought,salinity, extremes of temperature, chemical toxicity and oxidativestress. The ability to improve plant tolerance to abiotic stress wouldbe of great economic advantage to farmers worldwide and would allow forthe cultivation of crops during adverse conditions and in territorieswhere cultivation of crops may not otherwise be possible.

Crop yield may therefore be increased by optimising one of theabove-mentioned factors.

Depending on the end use, the modification of certain yield traits maybe favoured over others. For example for applications such as forage orwood production, or bio-fuel resource, an increase in the vegetativeparts of a plant may be desirable, and for applications such as flour,starch or oil production, an increase in seed parameters may beparticularly desirable. Even amongst the seed parameters, some may befavoured over others, depending on the application. Various mechanismsmay contribute to increasing seed yield, whether that is in the form ofincreased seed size or increased seed number.

One approach to increasing yield (seed yield and/or biomass) in plantsmay be through modification of the inherent growth mechanisms of aplant, such as the cell cycle or various signaling pathways involved inplant growth or in defence mechanisms.

It has now been found that various yield-related traits may be improvedin plants by modulating expression in a plant of a nucleic acid encodingan SGT1 polypeptide, or a CLC-pKG polypeptide, or a HD-hydrolase-likepolypeptide, in a plant.

BACKGROUND

1. SGT1 Polypeptides

SGT1 is known as a suppressor allele of skp1 mutant.

Chung et al., 2006 report that SGT1 plays a crucial role indevelopmental processes. SGT1 has unique domains necessary for proteinfunctions: tetratricopeptide repeat domain (TPR), CHORD and SGT1 motif(CS) and SGT1-specific motif (SGS motif). The TPR domain has been knownto mediate protein-protein interactions among multicomplex proteinsfunctioning as chaperone, cell cycle, transcription, or proteintransport complexes. For example, the TPR domain of SGT1 was shown tobind to heat-shock protein 70 (HSP70). However, the CS domain of SGT1 issimilar to the one in the human p23 protein, which is known to interactwith HSP90 and participate in the folding of different regulatoryproteins.

2. CLC-pKG Polypeptides

In both prokaryotic and eukaryotic organism, anion channels/transportersappear as key players in the control of metabolism, in the maintenanceof electrochemical gradients and in signaling pathways leading toadaptation to abiotic and biotic environmental stresses. In plants, theycontribute to various physiological functions such as control ofstomatal movements regulating gas exchanges in leaves, plant-pathogeninteraction, root xylem loading, compartmentation of metabolites andcoupling with proton gradients (reviewed in De Angeli et al. 2007 Phil.Trans. R. Soc. B 2009 364, 195-201). Anion channel activities andassociated regulation mechanisms have been characterized primarily usingelectrophysiological techniques. They were reported in all plantmembranes including the plasma membrane, tonoplast, endoplasmicreticulum, mitochondria and chloroplasts, plasma membrane channels beingby far the best characterized compared to those located on othermembranes. In model plants such as rice and Arabidopsis there are up toseven genes encoding CLCs which are spread in over two distinctsubfamilies (Marmagne et al. 2007, Journal of Experimental Botany, Vol.58, No. 12, pp. 3385-3393). One of such subfamilies comprising theAtCLCe and AtCLCf proteins is close to the prokaryotic CLC, altogetherbelonging to the Chloride Channel Prokaryotic Group while the otherclass is closer to the eukaryotic CLCs. The Arabidopsis thaliana AtCLCfprotein is reported to have similar subcellular distribution andpresumably similar function as those CLCs of Synechocystis CLC,considered to represent the ancestor precursor of plant chloroplast.

Nitrate and malate represent the majority of anions in a plant cell.Nitrate is a nutrient but can act as a signaling molecule as well.Plants have a sophisticated nitrate uptake system involving both low-and high-affinity transporters, nitrate is next either transportedthrough the xylem to enter into the cellular metabolism or is storedlocally. Cells assimilate nitrate via the nitrate reductase pathway orstore it in the tonoplast, and a dynamic balance exists betweencytosolic and vacuolar nitrate levels, regulated by uptake ofextracellular nitrate, storage in the vacuole and anabolism. Thediscovery of the chloride channel (CLC) family allowed unraveling themechanism of proton/nitrate exchange between tonoplasts and cytosol.Determination of subcellular localization, expression patterns, andcharacterization of knockout mutant phenotypes, gave insight in thephysiological role of CLC proteins. Phenotypic analyses showed thatclca-1 and clca-2 mutant plants have a reduced nitrate compared to thatof wild-type in root and shoot tissues. Also clcc and clce mutantsshowed lower nitrate levels compared to control plants. An overview ofthe art is provided by De Angeli et al., Phil. Trans. R. Soc. B 364,195-201, 2009; and the references cited therein. However, still littleis know about the precise role of CLC proteins, and the effect ofoverexpressing CLC genes on plant phenotypes.

3. HD-Hydrolase-Like Polypeptides

The HD domain comprises a sequence of two small amino acids, followed bytwo hydrophobic amino acids, a histidine and an aspartic acid, again ahydrophobic amino acid, a small amino acid and a charged amino acid.Because of its weak sequence conservation, it was only recentlydiscovered (Aravind and Koonin, Trends in Biochemical Sciences, 23:469-472, 1998). The domain is reportedly present in metal-dependentphosphohydrolases, including nucleic acid polymerases and helicases(Aravind and Koonin, 1998). Although the HD-domain comprising proteinsare predicted to exhibit phosphohydrolase activity and appears to beinvolved in nucleic acid metabolism or in signal transduction (Galperinet al., J. Mol. Microbiol Biotechnol. 1, 303-305, 1999), the precisebiological role of the HD domain remains to be elucidated.

SUMMARY

1. SGT1 Polypeptides

Surprisingly, it has now been found that modulating expression of anucleic acid encoding an SGT1 polypeptide gives plants having enhancedyield-related traits, in particular increased seed yield relative tocontrol plants.

According to one embodiment of the present invention, there is provideda method for improving yield-related traits in plants relative tocontrol plants, comprising modulating expression in a plant of a nucleicacid encoding an SGT1 polypeptide.

2. CLC-pKG Polypeptides

Surprisingly, it has now been found that modulating expression of anucleic acid encoding a CLC-pKG polypeptide gives plants having enhancedyield-related traits relative to control plants.

According one embodiment, there is provided a method for enhancing orimproving yield-related traits in plants relative to control plants,comprising modulating expression in a plant of a nucleic acid encoding aCLC-pKG polypeptide.

3. HD-Hydrolase-Like Polypeptides

Surprisingly, it has now been found that modulating expression of anucleic acid encoding a HD-hydrolase-like polypeptide gives plantshaving enhanced yield-related traits, in particular increased yieldrelative to control plants.

According one embodiment, there is provided a method for improvingyield-related traits in plants relative to control plants, comprisingmodulating expression in a plant of a nucleic acid encoding aHD-hydrolase-like polypeptide.

Definitions

The following definitions will be used throughout the presentspecification.

Polypeptide(s)/Protein(s)

The terms “polypeptide” and “protein” are used interchangeably hereinand refer to amino acids in a polymeric form of any length, linkedtogether by peptide bonds.

Polynucleotide(s)/Nucleic Acid(s)/Nucleic Acid Sequence(s)/NucleotideSequence(s)

The terms “polynucleotide(s)”, “nucleic acid sequence(s)”, “nucleotidesequence(s)”, “nucleic acid(s)”, “nucleic acid molecule” are usedinterchangeably herein and refer to nucleotides, either ribonucleotidesor deoxyribonucleotides or a combination of both, in a polymericunbranched form of any length.

Homologue(s)

“Homologues” of a protein encompass peptides, oligopeptides,polypeptides, proteins and enzymes having amino acid substitutions,deletions and/or insertions relative to the unmodified protein inquestion and having similar biological and functional activity as theunmodified protein from which they are derived.

A deletion refers to removal of one or more amino acids from a protein.

An insertion refers to one or more amino acid residues being introducedinto a predetermined site in a protein. Insertions may compriseN-terminal and/or C-terminal fusions as well as intra-sequenceinsertions of single or multiple amino acids. Generally, insertionswithin the amino acid sequence will be smaller than N- or C-terminalfusions, of the order of about 1 to 10 residues. Examples of N- orC-terminal fusion proteins or peptides include the binding domain oractivation domain of a transcriptional activator as used in the yeasttwo-hybrid system, phage coat proteins, (histidine)-6-tag, glutathioneS-transferase-tag, protein A, maltose-binding protein, dihydrofolatereductase, Tag·100 epitope, c-myc epitope, FLAG®-epitope, lacZ, CMP(calmodulin-binding peptide), HA epitope, protein C epitope and VSVepitope.

A substitution refers to replacement of amino acids of the protein withother amino acids having similar properties (such as similarhydrophobicity, hydrophilicity, antigenicity, propensity to form orbreak α-helical structures or β-sheet structures). Amino acidsubstitutions are typically of single residues, but may be clustereddepending upon functional constraints placed upon the polypeptide andmay range from 1 to 10 amino acids; insertions will usually be of theorder of about 1 to 10 amino acid residues. The amino acid substitutionsare preferably conservative amino acid substitutions. Conservativesubstitution tables are well known in the art (see for example Creighton(1984) Proteins. W.H. Freeman and Company (Eds) and Table 1 below).

TABLE 1 Examples of conserved amino acid substitutions ConservativeResidue Substitutions Ala Ser Arg Lys Asn Gln; His Asp Glu Gln Asn CysSer Glu Asp Gly Pro His Asn; Gln Ile Leu, Val Leu Ile; Val Lys Arg; GlnMet Leu; Ile Phe Met; Leu; Tyr Ser Thr; Gly Thr Ser; Val Trp Tyr TyrTrp; Phe Val Ile; Leu

Amino acid substitutions, deletions and/or insertions may readily bemade using peptide synthetic techniques well known in the art, such assolid phase peptide synthesis and the like, or by recombinant DNAmanipulation. Methods for the manipulation of DNA sequences to producesubstitution, insertion or deletion variants of a protein are well knownin the art. For example, techniques for making substitution mutations atpredetermined sites in DNA are well known to those skilled in the artand include M13 mutagenesis, T7-Gen in vitro mutagenesis (USB,Cleveland, Ohio), QuickChange Site Directed mutagenesis (Stratagene, SanDiego, Calif.), PCR-mediated site-directed mutagenesis or othersite-directed mutagenesis protocols.

Derivatives

“Derivatives” include peptides, oligopeptides, polypeptides which may,compared to the amino acid sequence of the naturally-occurring form ofthe protein, such as the protein of interest, comprise substitutions ofamino acids with non-naturally occurring amino acid residues, oradditions of non-naturally occurring amino acid residues. “Derivatives”of a protein also encompass peptides, oligopeptides, polypeptides whichcomprise naturally occurring altered (glycosylated, acylated,prenylated, phosphorylated, myristoylated, sulphated etc.) ornon-naturally altered amino acid residues compared to the amino acidsequence of a naturally-occurring form of the polypeptide. A derivativemay also comprise one or more non-amino acid substituents or additionscompared to the amino acid sequence from which it is derived, forexample a reporter molecule or other ligand, covalently ornon-covalently bound to the amino acid sequence, such as a reportermolecule which is bound to facilitate its detection, and non-naturallyoccurring amino acid residues relative to the amino acid sequence of anaturally-occurring protein. Furthermore, “derivatives” also includefusions of the naturally-occurring form of the protein with taggingpeptides such as FLAG, HIS6 or thioredoxin (for a review of taggingpeptides, see Terpe, Appl. Microbiol. Biotechnol. 60, 523-533, 2003).

Orthologue(s)/Paralogue(s)

Orthologues and paralogues encompass evolutionary concepts used todescribe the ancestral relationships of genes. Paralogues are geneswithin the same species that have originated through duplication of anancestral gene; orthologues are genes from different organisms that haveoriginated through speciation, and are also derived from a commonancestral gene.

Domain, Motif/Consensus Sequence/Signature

The term “domain” refers to a set of amino acids conserved at specificpositions along an alignment of sequences of evolutionarily relatedproteins. While amino acids at other positions can vary betweenhomologues, amino acids that are highly conserved at specific positionsindicate amino acids that are likely essential in the structure,stability or function of a protein. Identified by their high degree ofconservation in aligned sequences of a family of protein homologues,they can be used as identifiers to determine if any polypeptide inquestion belongs to a previously identified polypeptide family.

The term “motif” or “consensus sequence” or “signature” refers to ashort conserved region in the sequence of evolutionarily relatedproteins. Motifs are frequently highly conserved parts of domains, butmay also include only part of the domain, or be located outside ofconserved domain (if all of the amino acids of the motif fall outside ofa defined domain).

Specialist databases exist for the identification of domains, forexample, SMART (Schultz et al. (1998) Proc. Natl. Acad. Sci. USA 95,5857-5864; Letunic et al. (2002) Nucleic Acids Res 30, 242-244),InterPro (Mulder et al., (2003) Nucl. Acids. Res. 31, 315-318), Prosite(Bucher and Bairoch (1994), A generalized profile syntax forbiomolecular sequences motifs and its function in automatic sequenceinterpretation. (In) ISMB-94; Proceedings 2nd International Conferenceon Intelligent Systems for Molecular Biology. Altman R., Brutlag D.,Karp P., Lathrop R., Searls D., Eds., pp 53-61, AAAI Press, Menlo Park;Hulo et al., Nucl. Acids. Res. 32:D134-D137, (2004)), or Pfam (Batemanet al., Nucleic Acids Research 30(1): 276-280 (2002)). A set of toolsfor in silico analysis of protein sequences is available on the ExPASyproteomics server (Swiss Institute of Bioinformatics (Gasteiger et al.,ExPASy: the proteomics server for in-depth protein knowledge andanalysis, Nucleic Acids Res. 31:3784-3788(2003)). Domains or motifs mayalso be identified using routine techniques, such as by sequencealignment.

Methods for the alignment of sequences for comparison are well known inthe art, such methods include GAP, BESTFIT, BLAST, FASTA and TFASTA. GAPuses the algorithm of Needleman and Wunsch ((1970) J Mol Biol 48:443-453) to find the global (i.e. spanning the complete sequences)alignment of two sequences that maximizes the number of matches andminimizes the number of gaps. The BLAST algorithm (Altschul et al.(1990) J Mol Biol 215: 403-10) calculates percent sequence identity andperforms a statistical analysis of the similarity between the twosequences. The software for performing BLAST analysis is publiclyavailable through the National Centre for Biotechnology Information(NCBI). Homologues may readily be identified using, for example, theClustalW multiple sequence alignment algorithm (version 1.83), with thedefault pairwise alignment parameters, and a scoring method inpercentage. Global percentages of similarity and identity may also bedetermined using one of the methods available in the MatGAT softwarepackage (Campanella et al., BMC Bioinformatics. 2003 Jul. 10; 4:29.MatGAT: an application that generates similarity/identity matrices usingprotein or DNA sequences.). Minor manual editing may be performed tooptimise alignment between conserved motifs, as would be apparent to aperson skilled in the art. Furthermore, instead of using full-lengthsequences for the identification of homologues, specific domains mayalso be used. The sequence identity values may be determined over theentire nucleic acid or amino acid sequence or over selected domains orconserved motif(s), using the programs mentioned above using the defaultparameters. For local alignments, the Smith-Waterman algorithm isparticularly useful (Smith T F, Waterman M S (1981) J. Mol. Biol147(1);195-7).

Reciprocal BLAST

Typically, this involves a first BLAST involving BLASTing a querysequence (for example using any of the sequences listed in Table A ofthe Examples section) against any sequence database, such as thepublicly available NCBI database. BLASTN or TBLASTX (using standarddefault values) are generally used when starting from a nucleotidesequence, and BLASTP or TBLASTN (using standard default values) whenstarting from a protein sequence. The BLAST results may optionally befiltered. The full-length sequences of either the filtered results ornon-filtered results are then BLASTed back (second BLAST) againstsequences from the organism from which the query sequence is derived.The results of the first and second BLASTs are then compared. Aparalogue is identified if a high-ranking hit from the first blast isfrom the same species as from which the query sequence is derived, aBLAST back then ideally results in the query sequence amongst thehighest hits; an orthologue is identified if a high-ranking hit in thefirst BLAST is not from the same species as from which the querysequence is derived, and preferably results upon BLAST back in the querysequence being among the highest hits.

High-ranking hits are those having a low E-value. The lower the E-value,the more significant the score (or in other words the lower the chancethat the hit was found by chance). Computation of the E-value is wellknown in the art. In addition to E-values, comparisons are also scoredby percentage identity. Percentage identity refers to the number ofidentical nucleotides (or amino acids) between the two compared nucleicacid (or polypeptide) sequences over a particular length. In the case oflarge families, ClustalW may be used, followed by a neighbour joiningtree, to help visualize clustering of related genes and to identifyorthologues and paralogues.

Hybridisation

The term “hybridisation” as defined herein is a process whereinsubstantially homologous complementary nucleotide sequences anneal toeach other. The hybridisation process can occur entirely in solution,i.e. both complementary nucleic acids are in solution. The hybridisationprocess can also occur with one of the complementary nucleic acidsimmobilised to a matrix such as magnetic beads, Sepharose beads or anyother resin. The hybridisation process can furthermore occur with one ofthe complementary nucleic acids immobilised to a solid support such as anitro-cellulose or nylon membrane or immobilised by e.g.photolithography to, for example, a siliceous glass support (the latterknown as nucleic acid arrays or microarrays or as nucleic acid chips).In order to allow hybridisation to occur, the nucleic acid molecules aregenerally thermally or chemically denatured to melt a double strand intotwo single strands and/or to remove hairpins or other secondarystructures from single stranded nucleic acids.

The term “stringency” refers to the conditions under which ahybridisation takes place. The stringency of hybridisation is influencedby conditions such as temperature, salt concentration, ionic strengthand hybridisation buffer composition. Generally, low stringencyconditions are selected to be about 30° C. lower than the thermalmelting point (T_(m)) for the specific sequence at a defined ionicstrength and pH. Medium stringency conditions are when the temperatureis 20° C. below T_(m), and high stringency conditions are when thetemperature is 10° C. below T_(m). High stringency hybridisationconditions are typically used for isolating hybridising sequences thathave high sequence similarity to the target nucleic acid sequence.However, nucleic acids may deviate in sequence and still encode asubstantially identical polypeptide, due to the degeneracy of thegenetic code. Therefore medium stringency hybridisation conditions maysometimes be needed to identify such nucleic acid molecules.

The T_(m) is the temperature under defined ionic strength and pH, atwhich 50% of the target sequence hybridises to a perfectly matchedprobe. The T_(m) is dependent upon the solution conditions and the basecomposition and length of the probe. For example, longer sequenceshybridise specifically at higher temperatures. The maximum rate ofhybridisation is obtained from about 16° C. up to 32° C. below T_(m).The presence of monovalent cations in the hybridisation solution reducethe electrostatic repulsion between the two nucleic acid strands therebypromoting hybrid formation; this effect is visible for sodiumconcentrations of up to 0.4M (for higher concentrations, this effect maybe ignored). Formamide reduces the melting temperature of DNA-DNA andDNA-RNA duplexes with 0.6 to 0.7° C. for each percent formamide, andaddition of 50% formamide allows hybridisation to be performed at 30 to45° C., though the rate of hybridisation will be lowered. Base pairmismatches reduce the hybridisation rate and the thermal stability ofthe duplexes. On average and for large probes, the Tm decreases about 1°C. per % base mismatch. The T_(m) may be calculated using the followingequations, depending on the types of hybrids:

1) DNA-DNA hybrids (Meinkoth and Wahl, Anal. Biochem., 138: 267-284,1984):

T _(m)=81.5° C.+16.6x log₁₀[Na⁺]^(a)+0.41x %[G/C ^(b)]−500x[L^(c)]⁻¹−0.61x % formamide

2) DNA-RNA or RNA-RNA hybrids:

T _(m)=79.8° C.+18.5 (log₁₀[Na⁺]^(a))+0.58 (% G/C ^(b))+11.8 (% G/C^(b))²−820/L ^(c)

3) oligo-DNA or oligo-RNAs hybrids:

For <20 nucleotides: T _(m)=2 (l _(n))

For 20-35 nucleotides: T _(m)=22+1.46 (l _(n))

^(a) or for other monovalent cation, but only accurate in the 0.01-0.4 Mrange.

^(b) only accurate for % GC in the 30% to 75% range.

^(c) L=length of duplex in base pairs.

^(d) oligo, oligonucleotide; l_(n),=effective length of primer=2×(no. ofG/C)+(no. of A/T).

Non-specific binding may be controlled using any one of a number ofknown techniques such as, for example, blocking the membrane withprotein containing solutions, additions of heterologous RNA, DNA, andSDS to the hybridisation buffer, and treatment with Rnase. Fornon-homologous probes, a series of hybridizations may be performed byvarying one of (i) progressively lowering the annealing temperature (forexample from 68° C. to 42° C.) or (ii) progressively lowering theformamide concentration (for example from 50% to 0%). The skilledartisan is aware of various parameters which may be altered duringhybridisation and which will either maintain or change the stringencyconditions.

Besides the hybridisation conditions, specificity of hybridisationtypically also depends on the function of post-hybridisation washes. Toremove background resulting from non-specific hybridisation, samples arewashed with dilute salt solutions. Critical factors of such washesinclude the ionic strength and temperature of the final wash solution:the lower the salt concentration and the higher the wash temperature,the higher the stringency of the wash. Wash conditions are typicallyperformed at or below hybridisation stringency. A positive hybridisationgives a signal that is at least twice of that of the background.Generally, suitable stringent conditions for nucleic acid hybridisationassays or gene amplification detection procedures are as set forthabove. More or less stringent conditions may also be selected. Theskilled artisan is aware of various parameters which may be alteredduring washing and which will either maintain or change the stringencyconditions.

For example, typical high stringency hybridisation conditions for DNAhybrids longer than 50 nucleotides encompass hybridisation at 65° C. in1×SSC or at 42° C. in 1×SSC and 50% formamide, followed by washing at65° C. in 0.3×SSC. Examples of medium stringency hybridisationconditions for DNA hybrids longer than 50 nucleotides encompasshybridisation at 50° C. in 4×SSC or at 40° C. in 6×SSC and 50%formamide, followed by washing at 50° C. in 2×SSC. The length of thehybrid is the anticipated length for the hybridising nucleic acid. Whennucleic acids of known sequence are hybridised, the hybrid length may bedetermined by aligning the sequences and identifying the conservedregions described herein. 1×SSC is 0.15M NaCl and 15 mM sodium citrate;the hybridisation solution and wash solutions may additionally include5× Denhardt's reagent, 0.5-1.0% SDS, 100 μg/ml denatured, fragmentedsalmon sperm DNA, 0.5% sodium pyrophosphate.

For the purposes of defining the level of stringency, reference can bemade to Sambrook et al. (2001) Molecular Cloning: a laboratory manual,3^(rd) Edition, Cold Spring Harbor Laboratory Press, CSH, N.Y. or toCurrent Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989and yearly updates).

Splice Variant

The term “splice variant” as used herein encompasses variants of anucleic acid sequence in which selected introns and/or exons have beenexcised, replaced, displaced or added, or in which introns have beenshortened or lengthened. Such variants will be ones in which thebiological activity of the protein is substantially retained; this maybe achieved by selectively retaining functional segments of the protein.Such splice variants may be found in nature or may be manmade. Methodsfor predicting and isolating such splice variants are well known in theart (see for example Foissac and Schiex (2005) BMC Bioinformatics 6:25).

Allelic Variant

Alleles or allelic variants are alternative forms of a given gene,located at the same chromosomal position. Allelic variants encompassSingle Nucleotide Polymorphisms (SNPs), as well as SmallInsertion/Deletion Polymorphisms (INDELs). The size of INDELs is usuallyless than 100 bp. SNPs and INDELs form the largest set of sequencevariants in naturally occurring polymorphic strains of most organisms.

Endogenous Gene

Reference herein to an “endogenous” gene not only refers to the gene inquestion as found in a plant in its natural form (i.e., without therebeing any human intervention), but also refers to that same gene (or asubstantially homologous nucleic acid/gene) in an isolated formsubsequently (re)introduced into a plant (a transgene). For example, atransgenic plant containing such a transgene may encounter a substantialreduction of the transgene expression and/or substantial reduction ofexpression of the endogenous gene. The isolated gene may be isolatedfrom an organism or may be manmade, for example by chemical synthesis.

Gene Shuffling/Directed Evolution

Gene shuffling or directed evolution consists of iterations of DNAshuffling followed by appropriate screening and/or selection to generatevariants of nucleic acids or portions thereof encoding proteins having amodified biological activity (Castle et al., (2004) Science 304(5674):1151-4; U.S. Pat. Nos. 5,811,238 and 6,395,547).

Construct

Additional regulatory elements may include transcriptional as well astranslational enhancers. Those skilled in the art will be aware ofterminator and enhancer sequences that may be suitable for use inperforming the invention. An intron sequence may also be added to the 5′untranslated region (UTR) or in the coding sequence to increase theamount of the mature message that accumulates in the cytosol, asdescribed in the definitions section. Other control sequences (besidespromoter, enhancer, silencer, intron sequences, 3′UTR and/or 5′UTRregions) may be protein and/or RNA stabilizing elements. Such sequenceswould be known or may readily be obtained by a person skilled in theart.

The genetic constructs of the invention may further include an origin ofreplication sequence that is required for maintenance and/or replicationin a specific cell type. One example is when a genetic construct isrequired to be maintained in a bacterial cell as an episomal geneticelement (e.g. plasmid or cosmid molecule). Preferred origins ofreplication include, but are not limited to, the f1-ori and colE1.

For the detection of the successful transfer of the nucleic acidsequences as used in the methods of the invention and/or selection oftransgenic plants comprising these nucleic acids, it is advantageous touse marker genes (or reporter genes). Therefore, the genetic constructmay optionally comprise a selectable marker gene. Selectable markers aredescribed in more detail in the “definitions” section herein. The markergenes may be removed or excised from the transgenic cell once they areno longer needed. Techniques for marker removal are known in the art,useful techniques are described above in the definitions section.

Regulatory Element/Control Sequence/Promoter

The terms “regulatory element”, “control sequence” and “promoter” areall used interchangeably herein and are to be taken in a broad contextto refer to regulatory nucleic acid sequences capable of effectingexpression of the sequences to which they are ligated. The term“promoter” typically refers to a nucleic acid control sequence locatedupstream from the transcriptional start of a gene and which is involvedin recognising and binding of RNA polymerase and other proteins, therebydirecting transcription of an operably linked nucleic acid. Encompassedby the aforementioned terms are transcriptional regulatory sequencesderived from a classical eukaryotic genomic gene (including the TATA boxwhich is required for accurate transcription initiation, with or withouta CCAAT box sequence) and additional regulatory elements (i.e. upstreamactivating sequences, enhancers and silencers) which alter geneexpression in response to developmental and/or external stimuli, or in atissue-specific manner. Also included within the term is atranscriptional regulatory sequence of a classical prokaryotic gene, inwhich case it may include a −35 box sequence and/or −10 boxtranscriptional regulatory sequences. The term “regulatory element” alsoencompasses a synthetic fusion molecule or derivative that confers,activates or enhances expression of a nucleic acid molecule in a cell,tissue or organ.

A “plant promoter” comprises regulatory elements, which mediate theexpression of a coding sequence segment in plant cells. Accordingly, aplant promoter need not be of plant origin, but may originate fromviruses or micro-organisms, for example from viruses which attack plantcells. The “plant promoter” can also originate from a plant cell, e.g.from the plant which is transformed with the nucleic acid sequence to beexpressed in the inventive process and described herein. This alsoapplies to other “plant” regulatory signals, such as “plant”terminators. The promoters upstream of the nucleotide sequences usefulin the methods of the present invention can be modified by one or morenucleotide substitution(s), insertion(s) and/or deletion(s) withoutinterfering with the functionality or activity of either the promoters,the open reading frame (ORF) or the 3′-regulatory region such asterminators or other 3′ regulatory regions which are located away fromthe ORF. It is furthermore possible that the activity of the promotersis increased by modification of their sequence, or that they arereplaced completely by more active promoters, even promoters fromheterologous organisms. For expression in plants, the nucleic acidmolecule must, as described above, be linked operably to or comprise asuitable promoter which expresses the gene at the right point in timeand with the required spatial expression pattern.

For the identification of functionally equivalent promoters, thepromoter strength and/or expression pattern of a candidate promoter maybe analysed for example by operably linking the promoter to a reportergene and assaying the expression level and pattern of the reporter genein various tissues of the plant. Suitable well-known reporter genesinclude for example beta-glucuronidase or beta-galactosidase. Thepromoter activity is assayed by measuring the enzymatic activity of thebeta-glucuronidase or beta-galactosidase. The promoter strength and/orexpression pattern may then be compared to that of a reference promoter(such as the one used in the methods of the present invention).Alternatively, promoter strength may be assayed by quantifying mRNAlevels or by comparing mRNA levels of the nucleic acid used in themethods of the present invention, with mRNA levels of housekeeping genessuch as 18S rRNA, using methods known in the art, such as Northernblotting with densitometric analysis of autoradiograms, quantitativereal-time PCR or RT-PCR (Heid et al., 1996 Genome Methods 6: 986-994).Generally by “weak promoter” is intended a promoter that drivesexpression of a coding sequence at a low level. By “low level” isintended at levels of about 1/10,000 transcripts to about 1/100,000transcripts, to about 1/500,0000 transcripts per cell. Conversely, a“strong promoter” drives expression of a coding sequence at high level,or at about 1/10 transcripts to about 1/100 transcripts to about 1/1000transcripts per cell. Generally, by “medium strength promoter” isintended a promoter that drives expression of a coding sequence at alower level than a strong promoter, in particular at a level that is inall instances below that obtained when under the control of a 35S CaMVpromoter.

Operably Linked

The term “operably linked” as used herein refers to a functional linkagebetween the promoter sequence and the gene of interest, such that thepromoter sequence is able to initiate transcription of the gene ofinterest.

Constitutive Promoter

A “constitutive promoter” refers to a promoter that is transcriptionallyactive during most, but not necessarily all, phases of growth anddevelopment and under most environmental conditions, in at least onecell, tissue or organ. Table 2a below gives examples of constitutivepromoters.

TABLE 2a Examples of constitutive promoters Gene Source Reference ActinMcElroy et al, Plant Cell, 2: 163-171, 1990 HMGP WO 2004/070039 CAMV 35SOdell et al, Nature, 313: 810-812, 1985 CaMV 19S Nilsson et al.,Physiol. Plant. 100: 456-462, 1997 GOS2 de Pater et al, Plant J Nov;2(6): 837-44, 1992, WO 2004/065596 Ubiquitin Christensen et al, PlantMol. Biol. 18: 675-689, 1992 Rice cyclophilin Buchholz et al, Plant MolBiol. 25(5): 837-43, 1994 Maize H3 histone Lepetit et al, Mol. Gen.Genet. 231: 276-285, 1992 Alfalfa H3 histone Wu et al. Plant Mol. Biol.11: 641-649, 1988 Actin 2 An et al, Plant J. 10(1); 107-121, 1996 34SFMV Sanger et al., Plant. Mol. Biol., 14, 1990: 433-443 Rubisco smallU.S. Pat. No. 4,962,028 subunit OCS Leisner (1988) Proc Natl Acad SciUSA 85(5): 2553 SAD1 Jain et al., Crop Science, 39 (6), 1999: 1696 SAD2Jain et al., Crop Science, 39 (6), 1999: 1696 nos Shaw et al. (1984)Nucleic Acids Res. 12(20): 7831-7846 V-ATPase WO 01/14572 Super promoterWO 95/14098 G-box proteins WO 94/12015

Ubiquitous Promoter

A ubiquitous promoter is active in substantially all tissues or cells ofan organism.

Developmentally-Regulated Promoter

A developmentally-regulated promoter is active during certaindevelopmental stages or in parts of the plant that undergo developmentalchanges.

Inducible Promoter

An inducible promoter has induced or increased transcription initiationin response to a chemical (for a review see Gatz 1997, Annu. Rev. PlantPhysiol. Plant Mol. Biol., 48:89-108), environmental or physicalstimulus, or may be “stress-inducible”, i.e. activated when a plant isexposed to various stress conditions, or a “pathogen-inducible” i.e.activated when a plant is exposed to exposure to various pathogens.

Organ-Specific/Tissue-Specific Promoter

An organ-specific or tissue-specific promoter is one that is capable ofpreferentially initiating transcription in certain organs or tissues,such as the leaves, roots, seed tissue etc. For example, a“root-specific promoter” is a promoter that is transcriptionally activepredominantly in plant roots, substantially to the exclusion of anyother parts of a plant, whilst still allowing for any leaky expressionin these other plant parts. Promoters able to initiate transcription incertain cells only are referred to herein as “cell-specific”.

Examples of root-specific promoters are listed in Table 2b below:

TABLE 2b Examples of root-specific promoters Gene Source Reference RCc3Plant Mol Biol. 1995 January; 27(2): 237-48 Arabidopsis PHT1 Koyama etal. J Biosci Bioeng. 2005 January; 99(1): 38-42.; Mudge et al. (2002,Plant J. 31: 341) Medicago phosphate Xiao et al., 2006, Plant Biol(Stuttg). 2006 transporter July; 8(4): 439-49 Arabidopsis Pyk10 Nitz etal. (2001) Plant Sci 161(2): 337-346 root-expressible genes Tingey etal., EMBO J. 6: 1, 1987. tobacco auxin- Van der Zaal et al., Plant Mol.Biol. 16, 983, inducible gene 1991. β-tubulin Oppenheimer, et al., Gene63: 87, 1988. tobacco root-specific Conkling, et al., Plant Physiol. 93:1203, genes 1990. B. napus G1-3b gene U.S. Pat. No. 5,401,836 SbPRP1Suzuki et al., Plant Mol. Biol. 21: 109-119, 1993. LRX1 Baumberger etal. 2001, Genes & Dev. 15: 1128 BTG-26 Brassica napus US 20050044585LeAMT1 (tomato) Lauter et al. (1996, PNAS 3: 8139) The LeNRT1-1 (tomato)Lauter et al. (1996, PNAS 3: 8139) class I patatin gene Liu et al.,Plant Mol. Biol. 17 (6): (potato) 1139-1154 KDC1 (Daucus carota) Downeyet al. (2000, J. Biol. Chem. 275: 39420) TobRB7 gene W Song (1997) PhDThesis, North Carolina State University, Raleigh, NC USA OsRAB5a (rice)Wang et al. 2002, Plant Sci. 163: 273 ALF5 (Arabidopsis) Diener et al.(2001, Plant Cell 13: 1625) NRT2; 1Np Quesada et al. (1997, Plant Mol.Biol. 34: (N. plumbaginifolia) 265)

A seed-specific promoter is transcriptionally active predominantly inseed tissue, but not necessarily exclusively in seed tissue (in cases ofleaky expression). The seed-specific promoter may be active during seeddevelopment and/or during germination. The seed specific promoter may beendosperm/aleurone/embryo specific. Examples of seed-specific promoters(endosperm/aleurone/embryo specific) are shown in Table 2c to Table 2fbelow. Further examples of seed-specific promoters are given in Qing Quand Takaiwa (Plant Biotechnol. J. 2, 113-125, 2004), which disclosure isincorporated by reference herein as if fully set forth.

TABLE 2c Examples of seed-specific promoters Gene source Referenceseed-specific genes Simon et al., Plant Mol. Biol. 5: 191, 1985;Scofield et al., J. Biol. Chem. 262: 12202, 1987.; Baszczynski et al.,Plant Mol. Biol. 14: 633, 1990. Brazil Nut albumin Pearson et al., PlantMol. Biol. 18: 235-245, 1992. legumin Ellis et al., Plant Mol. Biol. 10:203-214, 1988. glutelin (rice) Takaiwa et al., Mol. Gen. Genet. 208:15-22, 1986; Takaiwa et al., FEBS Letts. 221: 43-47, 1987. zein Matzkeet al Plant Mol Biol, 14(3): 323-32 1990 napA Stalberg et al, Planta199: 515-519, 1996. wheat LMW and HMW Mol Gen Genet 216: 81-90, 1989;NAR 17: 461-2, 1989 glutenin-1 wheat SPA Albani et al, Plant Cell, 9:171-184, 1997 wheat α, β, γ-gliadins EMBO J. 3: 1409-15, 1984 barleyltr1 promoter Diaz et al. (1995) Mol Gen Genet 248(5): 592-8 barley B1,C, D, hordein Theor Appl Gen 98: 1253-62, 1999; Plant J 4: 343-55, 1993;Mol Gen Genet 250: 750-60, 1996 barley DOF Mena et al, The PlantJournal, 116(1): 53-62, 1998 blz2 EP99106056.7 synthetic promoterVicente-Carbajosa et al., Plant J. 13: 629-640, 1998. rice prolaminNRP33 Wu et al, Plant Cell Physiology 39(8) 885-889, 1998 ricea-globulin Glb-1 Wu et al, Plant Cell Physiology 39(8) 885-889, 1998rice OSH1 Sato et al, Proc. Natl. Acad. Sci. USA, 93: 8117-8122, 1996rice α-globulin REB/OHP-1 Nakase et al. Plant Mol. Biol. 33: 513-522,1997 rice ADP-glucose pyrophos- Trans Res 6: 157-68, 1997 phorylasemaize ESR gene family Plant J 12: 235-46, 1997 sorghum α-kafirin DeRoseet al., Plant Mol. Biol 32: 1029-35, 1996 KNOX Postma-Haarsma et al,Plant Mol. Biol. 39: 257-71, 1999 rice oleosin Wu et al, J. Biochem.123: 386, 1998 sunflower oleosin Cummins et al., Plant Mol. Biol. 19:873-876, 1992 PRO0117, putative rice 40S WO 2004/070039 ribosomalprotein PRO0136, rice alanine unpublished aminotransferase PRO0147,trypsin inhibitor unpublished ITR1 (barley) PRO0151, rice WSI18 WO2004/070039 PRO0175, rice RAB21 WO 2004/070039 PRO005 WO 2004/070039PRO0095 WO 2004/070039 α-amylase (Amy32b) Lanahan et al, Plant Cell 4:203-211, 1992; Skriver et al, Proc Natl Acad Sci USA 88: 7266-7270, 1991cathepsin β-like gene Cejudo et al, Plant Mol Biol 20: 849-856, 1992Barley Ltp2 Kalla et al., Plant J. 6: 849-60, 1994 Chi26 Leah et al.,Plant J. 4: 579-89, 1994 Maize B-Peru Selinger et al., Genetics 149;1125-38, 1998

TABLE 2d examples of endosperm-specific promoters Gene source Referenceglutelin (rice) Takaiwa et al. (1986) Mol Gen Genet 208: 15-22; Takaiwaet al. (1987) FEBS Letts. 221: 43-47 zein Matzke et al., (1990) PlantMol Biol 14(3): 323-32 wheat LMW and HMW glutenin-1 Colot et al. (1989)Mol Gen Genet 216: 81-90, Anderson et al. (1989) NAR 17: 461-2 wheat SPAAlbani et al. (1997) Plant Cell 9: 171-184 wheat gliadins Rafalski etal. (1984) EMBO 3: 1409-15 barley ltr1 promoter Diaz et al. (1995) MolGen Genet 248(5): 592-8 barley B1, C, D, hordein Cho et al. (1999) TheorAppl Genet 98: 1253-62; Muller et al. (1993) Plant J 4: 343-55; Sorensonet al. (1996) Mol Gen Genet 250: 750- 60 barley DOF Mena et al, (1998)Plant J 116(1): 53-62 blz2 Onate et al. (1999) J Biol Chem 274(14):9175-82 synthetic promoter Vicente-Carbajosa et al. (1998) Plant J 13:629- 640 rice prolamin NRP33 Wu et al, (1998) Plant Cell Physiol 39(8)885-889 rice globulin Glb-1 Wu et al. (1998) Plant Cell Physiol 39(8)885-889 rice globulin REB/OHP-1 Nakase et al. (1997) Plant Molec Biol33: 513-522 rice ADP-glucose Russell et al. (1997) Trans Res 6: 157-68pyrophosphorylase maize ESR gene family Opsahl-Ferstad et al. (1997)Plant J 12: 235-46 sorghum kafirin DeRose et al. (1996) Plant Mol Biol32: 1029-35

TABLE 2e Examples of embryo specific promoters: Gene source Referencerice OSH1 Sato et al, Proc. Natl. Acad. Sci. USA, 93: 8117-8122, 1996KNOX Postma-Haarsma et al, Plant Mol. Biol. 39: 257-71, 1999 PRO0151 WO2004/070039 PRO0175 WO 2004/070039 PRO005 WO 2004/070039 PRO0095 WO2004/070039

TABLE 2f Examples of aleurone-specific promoters: Gene source Referenceα-amylase (Amy32b) Lanahan et al, Plant Cell 4: 203-211, 1992; Skriveret al, Proc Natl Acad Sci USA 88: 7266-7270, 1991 cathepsin β-like geneCejudo et al, Plant Mol Biol 20: 849-856, 1992 Barley Ltp2 Kalla et al.,Plant J. 6: 849-60, 1994 Chi26 Leah et al., Plant J. 4: 579-89, 1994Maize B-Peru Selinger et al., Genetics 149; 1125-38, 1998

A green tissue-specific promoter as defined herein is a promoter that istranscriptionally active predominantly in green tissue, substantially tothe exclusion of any other parts of a plant, whilst still allowing forany leaky expression in these other plant parts.

Examples of green tissue-specific promoters which may be used to performthe methods of the invention are shown in Table 2g below.

TABLE 2g Examples of green tissue-specific promoters Gene ExpressionReference Maize Orthophosphate Leaf specific Fukavama et al., PlantPhysiol. dikinase 2001 November; 127(3): 1136-46 Maize Phosphoenol- Leafspecific Kausch et al., Plant Mol Biol. pyruvate carboxylase 2001January; 45(1): 1-15 Rice Phosphoenol- Leaf specific Lin et al., 2004DNA Seq. 2004 pyruvate carboxylase August; 15(4): 269-76 Rice smallsubunit Leaf specific Nomura et al., Plant Mol Biol. Rubisco 2000September; 44(1): 99-106 rice beta expansin Shoot WO 2004/070039 EXBP9specific Pigeonpea small subunit Leaf specific Panguluri et al., IndianJ Exp Rubisco Biol. 2005 April; 43(4): 369-72 Pea RBCS3A Leaf specific

Another example of a tissue-specific promoter is a meristem-specificpromoter, which is transcriptionally active predominantly inmeristematic tissue, substantially to the exclusion of any other partsof a plant, whilst still allowing for any leaky expression in theseother plant parts. Examples of green meristem-specific promoters whichmay be used to perform the methods of the invention are shown in Table2h below.

TABLE 2h Examples of meristem-specific promoters Gene source Expressionpattern Reference rice OSH1 Shoot apical meristem, Sato et al. (1996)Proc. from embryo globular stage Natl. Acad. Sci. USA, 93: to seedlingstage 8117-8122 Rice Meristem specific BAD87835.1 metallothionein WAK1 &Shoot and root apical Wagner & Kohorn (2001) WAK 2 meristems, and inPlant Cell 13(2): 303-318 expanding leaves and sepals

Terminator

The term “terminator” encompasses a control sequence which is a DNAsequence at the end of a transcriptional unit which signals 3′processing and polyadenylation of a primary transcript and terminationof transcription. The terminator can be derived from the natural gene,from a variety of other plant genes, or from T-DNA. The terminator to beadded may be derived from, for example, the nopaline synthase oroctopine synthase genes, or alternatively from another plant gene, orless preferably from any other eukaryotic gene.

Selectable Marker (Gene)/Reporter Gene

“Selectable marker”, “selectable marker gene” or “reporter gene”includes any gene that confers a phenotype on a cell in which it isexpressed to facilitate the identification and/or selection of cellsthat are transfected or transformed with a nucleic acid construct of theinvention. These marker genes enable the identification of a successfultransfer of the nucleic acid molecules via a series of differentprinciples. Suitable markers may be selected from markers that conferantibiotic or herbicide resistance, that introduce a new metabolic traitor that allow visual selection. Examples of selectable marker genesinclude genes conferring resistance to antibiotics (such as nptII thatphosphorylates neomycin and kanamycin, or hpt, phosphorylatinghygromycin, or genes conferring resistance to, for example, bleomycin,streptomycin, tetracyclin, chloramphenicol, ampicillin, gentamycin,geneticin (G418), spectinomycin or blasticidin), to herbicides (forexample bar which provides resistance to Basta®; aroA or gox providingresistance against glyphosate, or the genes conferring resistance to,for example, imidazolinone, phosphinothricin or sulfonylurea), or genesthat provide a metabolic trait (such as manA that allows plants to usemannose as sole carbon source or xylose isomerase for the utilisation ofxylose, or antinutritive markers such as the resistance to2-deoxyglucose). Expression of visual marker genes results in theformation of colour (for example β-glucuronidase, GUS or β-galactosidasewith its coloured substrates, for example X-Gal), luminescence (such asthe luciferin/luceferase system) or fluorescence (Green FluorescentProtein, GFP, and derivatives thereof). This list represents only asmall number of possible markers. The skilled worker is familiar withsuch markers. Different markers are preferred, depending on the organismand the selection method.

It is known that upon stable or transient integration of nucleic acidsinto plant cells, only a minority of the cells takes up the foreign DNAand, if desired, integrates it into its genome, depending on theexpression vector used and the transfection technique used. To identifyand select these integrants, a gene coding for a selectable marker (suchas the ones described above) is usually introduced into the host cellstogether with the gene of interest. These markers can for example beused in mutants in which these genes are not functional by, for example,deletion by conventional methods. Furthermore, nucleic acid moleculesencoding a selectable marker can be introduced into a host cell on thesame vector that comprises the sequence encoding the polypeptides of theinvention or used in the methods of the invention, or else in a separatevector. Cells which have been stably transfected with the introducednucleic acid can be identified for example by selection (for example,cells which have integrated the selectable marker survive whereas theother cells die).

Since the marker genes, particularly genes for resistance to antibioticsand herbicides, are no longer required or are undesired in thetransgenic host cell once the nucleic acids have been introducedsuccessfully, the process according to the invention for introducing thenucleic acids advantageously employs techniques which enable the removalor excision of these marker genes. One such a method is what is known asco-transformation. The co-transformation method employs two vectorssimultaneously for the transformation, one vector bearing the nucleicacid according to the invention and a second bearing the marker gene(s).A large proportion of transformants receives or, in the case of plants,comprises (up to 40% or more of the transformants), both vectors. Incase of transformation with Agrobacteria, the transformants usuallyreceive only a part of the vector, i.e. the sequence flanked by theT-DNA, which usually represents the expression cassette. The markergenes can subsequently be removed from the transformed plant byperforming crosses. In another method, marker genes integrated into atransposon are used for the transformation together with desired nucleicacid (known as the Ac/Ds technology). The transformants can be crossedwith a transposase source or the transformants are transformed with anucleic acid construct conferring expression of a transposase,transiently or stable. In some cases (approx. 10%), the transposon jumpsout of the genome of the host cell once transformation has taken placesuccessfully and is lost. In a further number of cases, the transposonjumps to a different location. In these cases the marker gene must beeliminated by performing crosses. In microbiology, techniques weredeveloped which make possible, or facilitate, the detection of suchevents. A further advantageous method relies on what is known asrecombination systems; whose advantage is that elimination by crossingcan be dispensed with. The best-known system of this type is what isknown as the Cre/lox system. Cre1 is a recombinase that removes thesequences located between the loxP sequences. If the marker gene isintegrated between the loxP sequences, it is removed once transformationhas taken place successfully, by expression of the recombinase. Furtherrecombination systems are the HIN/HIX, FLP/FRT and REP/STB system(Tribble et al., J. Biol. Chem., 275, 2000: 22255-22267; Velmurugan etal., J. Cell Biol., 149, 2000: 553-566). A site-specific integrationinto the plant genome of the nucleic acid sequences according to theinvention is possible. Naturally, these methods can also be applied tomicroorganisms such as yeast, fungi or bacteria.

Transgenic/Transgene/Recombinant

For the purposes of the invention, “transgenic”, “transgene” or“recombinant” means with regard to, for example, a nucleic acidsequence, an expression cassette, gene construct or a vector comprisingthe nucleic acid sequence or an organism transformed with the nucleicacid sequences, expression cassettes or vectors according to theinvention, all those constructions brought about by recombinant methodsin which either

-   -   (a) the nucleic acid sequences encoding proteins useful in the        methods of the invention, or    -   (b) genetic control sequence(s) which is operably linked with        the nucleic acid sequence according to the invention, for        example a promoter, or    -   (c) a) and b)

are not located in their natural genetic environment or have beenmodified by recombinant methods, it being possible for the modificationto take the form of, for example, a substitution, addition, deletion,inversion or insertion of one or more nucleotide residues. The naturalgenetic environment is understood as meaning the natural genomic orchromosomal locus in the original plant or the presence in a genomiclibrary. In the case of a genomic library, the natural geneticenvironment of the nucleic acid sequence is preferably retained, atleast in part. The environment flanks the nucleic acid sequence at leaston one side and has a sequence length of at least 50 bp, preferably atleast 500 bp, especially preferably at least 1000 bp, most preferably atleast 5000 bp. A naturally occurring expression cassette—for example thenaturally occurring combination of the natural promoter of the nucleicacid sequences with the corresponding nucleic acid sequence encoding apolypeptide useful in the methods of the present invention, as definedabove—becomes a transgenic expression cassette when this expressioncassette is modified by non-natural, synthetic (“artificial”) methodssuch as, for example, mutagenic treatment. Suitable methods aredescribed, for example, in U.S. Pat. No. 5,565,350 or WO 00/15815.

A transgenic plant for the purposes of the invention is thus understoodas meaning, as above, that the nucleic acids used in the method of theinvention are not present in, or originating from, the genome of saidplant, or are present in the genome of said plant but not at theirnatural locus in the genome of said plant, it being possible for thenucleic acids to be expressed homologously or heterologously. However,as mentioned, transgenic also means that, while the nucleic acidsaccording to the invention or used in the inventive method are at theirnatural position in the genome of a plant, the sequence has beenmodified with regard to the natural sequence, and/or that the regulatorysequences of the natural sequences have been modified. Transgenic ispreferably understood as meaning the expression of the nucleic acidsaccording to the invention at an unnatural locus in the genome, i.e.homologous or, preferably, heterologous expression of the nucleic acidstakes place. Preferred transgenic plants are mentioned herein.

It shall further be noted that in the context of the present invention,the term “isolated nucleic acid” or “isolated polypeptide” may in someinstances be considered as a synonym for a “recombinant nucleic acid” ora “recombinant polypeptide”, respectively and refers to a nucleic acidor polypeptide that is not located in its natural genetic environmentand/or that has been modified by recombinant methods.

Modulation

The term “modulation” means in relation to expression or geneexpression, a process in which the expression level is changed by saidgene expression in comparison to the control plant, the expression levelmay be increased or decreased. The original, unmodulated expression maybe of any kind of expression of a structural RNA (rRNA, tRNA) or mRNAwith subsequent translation. For the purposes of this invention, theoriginal unmodulated expression may also be absence of any expression.The term “modulating the activity” shall mean any change of theexpression of the inventive nucleic acid sequences or encoded proteins,which leads to increased yield and/or increased growth of the plants.The expression can increase from zero (absence of, or immeasurableexpression) to a certain amount, or can decrease from a certain amountto immeasurable small amounts or zero.

Expression

The term “expression” or “gene expression” means the transcription of aspecific gene or specific genes or specific genetic construct. The term“expression” or “gene expression” in particular means the transcriptionof a gene or genes or genetic construct into structural RNA (rRNA, tRNA)or mRNA with or without subsequent translation of the latter into aprotein. The process includes transcription of DNA and processing of theresulting mRNA product.

Increased Expression/Overexpression

The term “increased expression” or “overexpression” as used herein meansany form of expression that is additional to the original wild-typeexpression level. For the purposes of this invention, the originalwild-type expression level might also be zero, i.e. absence ofexpression or immeasurable expression.

Methods for increasing expression of genes or gene products are welldocumented in the art and include, for example, overexpression driven byappropriate promoters, the use of transcription enhancers or translationenhancers. Isolated nucleic acids which serve as promoter or enhancerelements may be introduced in an appropriate position (typicallyupstream) of a non-heterologous form of a polynucleotide so as toupregulate expression of a nucleic acid encoding the polypeptide ofinterest. For example, endogenous promoters may be altered in vivo bymutation, deletion, and/or substitution (see, Kmiec, U.S. Pat. No.5,565,350; Zarling et al., WO9322443), or isolated promoters may beintroduced into a plant cell in the proper orientation and distance froma gene of the present invention so as to control the expression of thegene.

If polypeptide expression is desired, it is generally desirable toinclude a polyadenylation region at the 3′-end of a polynucleotidecoding region. The polyadenylation region can be derived from thenatural gene, from a variety of other plant genes, or from T-DNA. The 3′end sequence to be added may be derived from, for example, the nopalinesynthase or octopine synthase genes, or alternatively from another plantgene, or less preferably from any other eukaryotic gene.

An intron sequence may also be added to the 5′ untranslated region (UTR)or the coding sequence of the partial coding sequence to increase theamount of the mature message that accumulates in the cytosol. Inclusionof a spliceable intron in the transcription unit in both plant andanimal expression constructs has been shown to increase gene expressionat both the mRNA and protein levels up to 1000-fold (Buchman and Berg(1988) Mol. Cell biol. 8: 4395-4405; Callis et al. (1987) Genes Dev1:1183-1200). Such intron enhancement of gene expression is typicallygreatest when placed near the 5′ end of the transcription unit. Use ofthe maize introns Adh1-S intron 1, 2, and 6, the Bronze-1 intron areknown in the art. For general information see: The Maize Handbook,Chapter 116, Freeling and Walbot, Eds., Springer, N.Y. (1994).

Decreased Expression

Reference herein to “decreased expression” or “reduction or substantialelimination” of expression is taken to mean a decrease in endogenousgene expression and/or polypeptide levels and/or polypeptide activityrelative to control plants. The reduction or substantial elimination isin increasing order of preference at least 10%, 20%, 30%, 40% or 50%,60%, 70%, 80%, 85%, 90%, or 95%, 96%, 97%, 98%, 99% or more reducedcompared to that of control plants.

For the reduction or substantial elimination of expression an endogenousgene in a plant, a sufficient length of substantially contiguousnucleotides of a nucleic acid sequence is required. In order to performgene silencing, this may be as little as 20, 19, 18, 17, 16, 15, 14, 13,12, 11, 10 or fewer nucleotides, alternatively this may be as much asthe entire gene (including the 5′ and/or 3′ UTR, either in part or inwhole). The stretch of substantially contiguous nucleotides may bederived from the nucleic acid encoding the protein of interest (targetgene), or from any nucleic acid capable of encoding an orthologue,paralogue or homologue of the protein of interest. Preferably, thestretch of substantially contiguous nucleotides is capable of forminghydrogen bonds with the target gene (either sense or antisense strand),more preferably, the stretch of substantially contiguous nucleotideshas, in increasing order of preference, 50%, 60%, 70%, 80%, 85%, 90%,95%, 96%, 97%, 98%, 99%, 100% sequence identity to the target gene(either sense or antisense strand). A nucleic acid sequence encoding a(functional) polypeptide is not a requirement for the various methodsdiscussed herein for the reduction or substantial elimination ofexpression of an endogenous gene.

This reduction or substantial elimination of expression may be achievedusing routine tools and techniques. A preferred method for the reductionor substantial elimination of endogenous gene expression is byintroducing and expressing in a plant a genetic construct into which thenucleic acid (in this case a stretch of substantially contiguousnucleotides derived from the gene of interest, or from any nucleic acidcapable of encoding an orthologue, paralogue or homologue of any one ofthe protein of interest) is cloned as an inverted repeat (in part orcompletely), separated by a spacer (non-coding DNA).

In such a preferred method, expression of the endogenous gene is reducedor substantially eliminated through RNA-mediated silencing using aninverted repeat of a nucleic acid or a part thereof (in this case astretch of substantially contiguous nucleotides derived from the gene ofinterest, or from any nucleic acid capable of encoding an orthologue,paralogue or homologue of the protein of interest), preferably capableof forming a hairpin structure. The inverted repeat is cloned in anexpression vector comprising control sequences. A non-coding DNA nucleicacid sequence (a spacer, for example a matrix attachment region fragment(MAR), an intron, a polylinker, etc.) is located between the twoinverted nucleic acids forming the inverted repeat. After transcriptionof the inverted repeat, a chimeric RNA with a self-complementarystructure is formed (partial or complete). This double-stranded RNAstructure is referred to as the hairpin RNA (hpRNA). The hpRNA isprocessed by the plant into siRNAs that are incorporated into anRNA-induced silencing complex (RISC). The RISC further cleaves the mRNAtranscripts, thereby substantially reducing the number of mRNAtranscripts to be translated into polypeptides. For further generaldetails see for example, Grierson et al. (1998) WO 98/53083; Waterhouseet al. (1999) WO 99/53050).

Performance of the methods of the invention does not rely on introducingand expressing in a plant a genetic construct into which the nucleicacid is cloned as an inverted repeat, but any one or more of severalwell-known “gene silencing” methods may be used to achieve the sameeffects.

One such method for the reduction of endogenous gene expression isRNA-mediated silencing of gene expression (downregulation). Silencing inthis case is triggered in a plant by a double stranded RNA sequence(dsRNA) that is substantially similar to the target endogenous gene.This dsRNA is further processed by the plant into about 20 to about 26nucleotides called short interfering RNAs (siRNAs). The siRNAs areincorporated into an RNA-induced silencing complex (RISC) that cleavesthe mRNA transcript of the endogenous target gene, thereby substantiallyreducing the number of mRNA transcripts to be translated into apolypeptide. Preferably, the double stranded RNA sequence corresponds toa target gene.

Another example of an RNA silencing method involves the introduction ofnucleic acid sequences or parts thereof (in this case a stretch ofsubstantially contiguous nucleotides derived from the gene of interest,or from any nucleic acid capable of encoding an orthologue, paralogue orhomologue of the protein of interest) in a sense orientation into aplant. “Sense orientation” refers to a DNA sequence that is homologousto an mRNA transcript thereof. Introduced into a plant would thereforebe at least one copy of the nucleic acid sequence. The additionalnucleic acid sequence will reduce expression of the endogenous gene,giving rise to a phenomenon known as co-suppression. The reduction ofgene expression will be more pronounced if several additional copies ofa nucleic acid sequence are introduced into the plant, as there is apositive correlation between high transcript levels and the triggeringof co-suppression.

Another example of an RNA silencing method involves the use of antisensenucleic acid sequences. An “antisense” nucleic acid sequence comprises anucleotide sequence that is complementary to a “sense” nucleic acidsequence encoding a protein, i.e. complementary to the coding strand ofa double-stranded cDNA molecule or complementary to an mRNA transcriptsequence. The antisense nucleic acid sequence is preferablycomplementary to the endogenous gene to be silenced. The complementaritymay be located in the “coding region” and/or in the “non-coding region”of a gene. The term “coding region” refers to a region of the nucleotidesequence comprising codons that are translated into amino acid residues.The term “non-coding region” refers to 5′ and 3′ sequences that flankthe coding region that are transcribed but not translated into aminoacids (also referred to as 5′ and 3′ untranslated regions).

Antisense nucleic acid sequences can be designed according to the rulesof Watson and Crick base pairing. The antisense nucleic acid sequencemay be complementary to the entire nucleic acid sequence (in this case astretch of substantially contiguous nucleotides derived from the gene ofinterest, or from any nucleic acid capable of encoding an orthologue,paralogue or homologue of the protein of interest), but may also be anoligonucleotide that is antisense to only a part of the nucleic acidsequence (including the mRNA 5′ and 3′ UTR). For example, the antisenseoligonucleotide sequence may be complementary to the region surroundingthe translation start site of an mRNA transcript encoding a polypeptide.The length of a suitable antisense oligonucleotide sequence is known inthe art and may start from about 50, 45, 40, 35, 30, 25, 20, 15 or 10nucleotides in length or less. An antisense nucleic acid sequenceaccording to the invention may be constructed using chemical synthesisand enzymatic ligation reactions using methods known in the art. Forexample, an antisense nucleic acid sequence (e.g., an antisenseoligonucleotide sequence) may be chemically synthesized using naturallyoccurring nucleotides or variously modified nucleotides designed toincrease the biological stability of the molecules or to increase thephysical stability of the duplex formed between the antisense and sensenucleic acid sequences, e.g., phosphorothioate derivatives and acridinesubstituted nucleotides may be used. Examples of modified nucleotidesthat may be used to generate the antisense nucleic acid sequences arewell known in the art. Known nucleotide modifications includemethylation, cyclization and ‘caps’ and substitution of one or more ofthe naturally occurring nucleotides with an analogue such as inosine.Other modifications of nucleotides are well known in the art.

The antisense nucleic acid sequence can be produced biologically usingan expression vector into which a nucleic acid sequence has beensubcloned in an antisense orientation (i.e., RNA transcribed from theinserted nucleic acid will be of an antisense orientation to a targetnucleic acid of interest). Preferably, production of antisense nucleicacid sequences in plants occurs by means of a stably integrated nucleicacid construct comprising a promoter, an operably linked antisenseoligonucleotide, and a terminator.

The nucleic acid molecules used for silencing in the methods of theinvention (whether introduced into a plant or generated in situ)hybridize with or bind to mRNA transcripts and/or genomic DNA encoding apolypeptide to thereby inhibit expression of the protein, e.g., byinhibiting transcription and/or translation. The hybridization can be byconventional nucleotide complementarity to form a stable duplex, or, forexample, in the case of an antisense nucleic acid sequence which bindsto DNA duplexes, through specific interactions in the major groove ofthe double helix. Antisense nucleic acid sequences may be introducedinto a plant by transformation or direct injection at a specific tissuesite. Alternatively, antisense nucleic acid sequences can be modified totarget selected cells and then administered systemically. For example,for systemic administration, antisense nucleic acid sequences can bemodified such that they specifically bind to receptors or antigensexpressed on a selected cell surface, e.g., by linking the antisensenucleic acid sequence to peptides or antibodies which bind to cellsurface receptors or antigens. The antisense nucleic acid sequences canalso be delivered to cells using the vectors described herein.

According to a further aspect, the antisense nucleic acid sequence is ana-anomeric nucleic acid sequence. An a-anomeric nucleic acid sequenceforms specific double-stranded hybrids with complementary RNA in which,contrary to the usual b-units, the strands run parallel to each other(Gaultier et al. (1987) Nucl Ac Res 15: 6625-6641). The antisensenucleic acid sequence may also comprise a 2′-o-methylribonucleotide(Inoue et al. (1987) Nucl Ac Res 15, 6131-6148) or a chimeric RNA-DNAanalogue (Inoue et al. (1987) FEBS Lett. 215, 327-330).

The reduction or substantial elimination of endogenous gene expressionmay also be performed using ribozymes. Ribozymes are catalytic RNAmolecules with ribonuclease activity that are capable of cleaving asingle-stranded nucleic acid sequence, such as an mRNA, to which theyhave a complementary region. Thus, ribozymes (e.g., hammerhead ribozymes(described in Haselhoff and Gerlach (1988) Nature 334, 585-591) can beused to catalytically cleave mRNA transcripts encoding a polypeptide,thereby substantially reducing the number of mRNA transcripts to betranslated into a polypeptide. A ribozyme having specificity for anucleic acid sequence can be designed (see for example: Cech et al. U.S.Pat. No. 4,987,071; and Cech et al. U.S. Pat. No. 5,116,742).Alternatively, mRNA transcripts corresponding to a nucleic acid sequencecan be used to select a catalytic RNA having a specific ribonucleaseactivity from a pool of RNA molecules (Bartel and Szostak (1993) Science261, 1411-1418). The use of ribozymes for gene silencing in plants isknown in the art (e.g., Atkins et al. (1994) WO 94/00012; Lenne et al.(1995) WO 95/03404; Lutziger et al. (2000) WO 00/00619; Prinsen et al.(1997) WO 97/13865 and Scott et al. (1997) WO 97/38116).

Gene silencing may also be achieved by insertion mutagenesis (forexample, T-DNA insertion or transposon insertion) or by strategies asdescribed by, among others, Angell and Baulcombe ((1999) Plant J 20(3):357-62), (Amplicon VIGS WO 98/36083), or Baulcombe (WO 99/15682).

Gene silencing may also occur if there is a mutation on an endogenousgene and/or a mutation on an isolated gene/nucleic acid subsequentlyintroduced into a plant. The reduction or substantial elimination may becaused by a non-functional polypeptide. For example, the polypeptide maybind to various interacting proteins; one or more mutation(s) and/ortruncation(s) may therefore provide for a polypeptide that is still ableto bind interacting proteins (such as receptor proteins) but that cannotexhibit its normal function (such as signaling ligand).

A further approach to gene silencing is by targeting nucleic acidsequences complementary to the regulatory region of the gene (e.g., thepromoter and/or enhancers) to form triple helical structures thatprevent transcription of the gene in target cells. See Helene, C.,Anticancer Drug Res. 6, 569-84, 1991; Helene et al., Ann. N.Y. Acad.Sci. 660, 27-36 1992; and Maher, L. J. Bioassays 14, 807-15, 1992.

Other methods, such as the use of antibodies directed to an endogenouspolypeptide for inhibiting its function in planta, or interference inthe signaling pathway in which a polypeptide is involved, will be wellknown to the skilled man. In particular, it can be envisaged thatmanmade molecules may be useful for inhibiting the biological functionof a target polypeptide, or for interfering with the signaling pathwayin which the target polypeptide is involved.

Alternatively, a screening program may be set up to identify in a plantpopulation natural variants of a gene, which variants encodepolypeptides with reduced activity. Such natural variants may also beused for example, to perform homologous recombination.

Artificial and/or natural microRNAs (miRNAs) may be used to knock outgene expression and/or mRNA translation. Endogenous miRNAs are singlestranded small RNAs of typically 19-24 nucleotides long. They functionprimarily to regulate gene expression and/or mRNA translation. Mostplant microRNAs (miRNAs) have perfect or near-perfect complementaritywith their target sequences. However, there are natural targets with upto five mismatches. They are processed from longer non-coding RNAs withcharacteristic fold-back structures by double-strand specific RNases ofthe Dicer family. Upon processing, they are incorporated in theRNA-induced silencing complex (RISC) by binding to its main component,an Argonaute protein. MiRNAs serve as the specificity components ofRISC, since they base-pair to target nucleic acids, mostly mRNAs, in thecytoplasm. Subsequent regulatory events include target mRNA cleavage anddestruction and/or translational inhibition. Effects of miRNAoverexpression are thus often reflected in decreased mRNA levels oftarget genes.

Artificial microRNAs (amiRNAs), which are typically 21 nucleotides inlength, can be genetically engineered specifically to negativelyregulate gene expression of single or multiple genes of interest.Determinants of plant microRNA target selection are well known in theart. Empirical parameters for target recognition have been defined andcan be used to aid in the design of specific amiRNAs, (Schwab et al.,Dev. Cell 8, 517-527, 2005). Convenient tools for design and generationof amiRNAs and their precursors are also available to the public (Schwabet al., Plant Cell 18, 1121-1133, 2006).

For optimal performance, the gene silencing techniques used for reducingexpression in a plant of an endogenous gene requires the use of nucleicacid sequences from monocotyledonous plants for transformation ofmonocotyledonous plants, and from dicotyledonous plants fortransformation of dicotyledonous plants. Preferably, a nucleic acidsequence from any given plant species is introduced into that samespecies. For example, a nucleic acid sequence from rice is transformedinto a rice plant. However, it is not an absolute requirement that thenucleic acid sequence to be introduced originates from the same plantspecies as the plant in which it will be introduced. It is sufficientthat there is substantial homology between the endogenous target geneand the nucleic acid to be introduced.

Described above are examples of various methods for the reduction orsubstantial elimination of expression in a plant of an endogenous gene.A person skilled in the art would readily be able to adapt theaforementioned methods for silencing so as to achieve reduction ofexpression of an endogenous gene in a whole plant or in parts thereofthrough the use of an appropriate promoter, for example.

Transformation

The term “introduction” or “transformation” as referred to hereinencompasses the transfer of an exogenous polynucleotide into a hostcell, irrespective of the method used for transfer. Plant tissue capableof subsequent clonal propagation, whether by organogenesis orembryogenesis, may be transformed with a genetic construct of thepresent invention and a whole plant regenerated there from. Theparticular tissue chosen will vary depending on the clonal propagationsystems available for, and best suited to, the particular species beingtransformed. Exemplary tissue targets include leaf disks, pollen,embryos, cotyledons, hypocotyls, megagametophytes, callus tissue,existing meristematic tissue (e.g., apical meristem, axillary buds, androot meristems), and induced meristem tissue (e.g., cotyledon meristemand hypocotyl meristem). The polynucleotide may be transiently or stablyintroduced into a host cell and may be maintained non-integrated, forexample, as a plasmid. Alternatively, it may be integrated into the hostgenome. The resulting transformed plant cell may then be used toregenerate a transformed plant in a manner known to persons skilled inthe art.

The transfer of foreign genes into the genome of a plant is calledtransformation. Transformation of plant species is now a fairly routinetechnique. Advantageously, any of several transformation methods may beused to introduce the gene of interest into a suitable ancestor cell.The methods described for the transformation and regeneration of plantsfrom plant tissues or plant cells may be utilized for transient or forstable transformation. Transformation methods include the use ofliposomes, electroporation, chemicals that increase free DNA uptake,injection of the DNA directly into the plant, particle gun bombardment,transformation using viruses or pollen and microprojection. Methods maybe selected from the calcium/polyethylene glycol method for protoplasts(Krens, F. A. et al., (1982) Nature 296, 72-74; Negrutiu I et al. (1987)Plant Mol Biol 8: 363-373); electroporation of protoplasts (Shillito R.D. et al. (1985) Bio/Technol 3, 1099-1102); microinjection into plantmaterial (Crossway A et al., (1986) Mol. Gen Genet 202: 179-185); DNA orRNA-coated particle bombardment (Klein T M et al., (1987) Nature 327:70) infection with (non-integrative) viruses and the like. Transgenicplants, including transgenic crop plants, are preferably produced viaAgrobacterium-mediated transformation. An advantageous transformationmethod is the transformation in planta. To this end, it is possible, forexample, to allow the agrobacteria to act on plant seeds or to inoculatethe plant meristem with agrobacteria. It has proved particularlyexpedient in accordance with the invention to allow a suspension oftransformed agrobacteria to act on the intact plant or at least on theflower primordia. The plant is subsequently grown on until the seeds ofthe treated plant are obtained (Clough and Bent, Plant J. (1998) 16,735-743). Methods for Agrobacterium-mediated transformation of riceinclude well known methods for rice transformation, such as thosedescribed in any of the following: European patent application EP1198985 A1, Aldemita and Hodges (Planta 199: 612-617, 1996); Chan et al.(Plant Mol Biol 22 (3): 491-506, 1993), Hiei et al. (Plant J 6 (2):271-282, 1994), which disclosures are incorporated by reference hereinas if fully set forth. In the case of corn transformation, the preferredmethod is as described in either Ishida et al. (Nat. Biotechnol 14(6):745-50, 1996) or Frame et al. (Plant Physiol 129(1): 13-22, 2002), whichdisclosures are incorporated by reference herein as if fully set forth.Said methods are further described by way of example in B. Jenes et al.,Techniques for Gene Transfer, in: Transgenic Plants, Vol. 1, Engineeringand Utilization, eds. S. D. Kung and R. Wu, Academic Press (1993)128-143 and in Potrykus Annu. Rev. Plant Physiol. Plant Molec. Biol. 42(1991) 205-225). The nucleic acids or the construct to be expressed ispreferably cloned into a vector, which is suitable for transformingAgrobacterium tumefaciens, for example pBin19 (Bevan et al., Nucl. AcidsRes. 12 (1984) 8711). Agrobacteria transformed by such a vector can thenbe used in known manner for the transformation of plants, such as plantsused as a model, like Arabidopsis (Arabidopsis thaliana is within thescope of the present invention not considered as a crop plant), or cropplants such as, by way of example, tobacco plants, for example byimmersing bruised leaves or chopped leaves in an agrobacterial solutionand then culturing them in suitable media. The transformation of plantsby means of Agrobacterium tumefaciens is described, for example, byHöfgen and Willmitzer in Nucl. Acid Res. (1988) 16, 9877 or is knowninter alia from F. F. White, Vectors for Gene Transfer in Higher Plants;in Transgenic Plants, Vol. 1, Engineering and Utilization, eds. S. D.Kung and R. Wu, Academic Press, 1993, pp. 15-38.

In addition to the transformation of somatic cells, which then have tobe regenerated into intact plants, it is also possible to transform thecells of plant meristems and in particular those cells which developinto gametes. In this case, the transformed gametes follow the naturalplant development, giving rise to transgenic plants. Thus, for example,seeds of Arabidopsis are treated with agrobacteria and seeds areobtained from the developing plants of which a certain proportion istransformed and thus transgenic [Feldman, K A and Marks M D (1987). MolGen Genet 208:1-9; Feldmann K (1992). In: C Koncz, N-H Chua and J Shell,eds, Methods in Arabidopsis Research. Word Scientific, Singapore, pp.274-289]. Alternative methods are based on the repeated removal of theinflorescences and incubation of the excision site in the center of therosette with transformed agrobacteria, whereby transformed seeds canlikewise be obtained at a later point in time (Chang (1994). Plant J. 5:551-558; Katavic (1994). Mol Gen Genet, 245: 363-370). However, anespecially effective method is the vacuum infiltration method with itsmodifications such as the “floral dip” method. In the case of vacuuminfiltration of Arabidopsis, intact plants under reduced pressure aretreated with an agrobacterial suspension [Bechthold, N (1993). C R AcadSci Paris Life Sci, 316: 1194-1199], while in the case of the “floraldip” method the developing floral tissue is incubated briefly with asurfactant-treated agrobacterial suspension [Clough, S J and Bent A F(1998) The Plant J. 16, 735-743]. A certain proportion of transgenicseeds are harvested in both cases, and these seeds can be distinguishedfrom non-transgenic seeds by growing under the above-described selectiveconditions. In addition the stable transformation of plastids is ofadvantages because plastids are inherited maternally is most cropsreducing or eliminating the risk of transgene flow through pollen. Thetransformation of the chloroplast genome is generally achieved by aprocess which has been schematically displayed in Klaus et al., 2004[Nature Biotechnology 22 (2), 225-229]. Briefly the sequences to betransformed are cloned together with a selectable marker gene betweenflanking sequences homologous to the chloroplast genome. Thesehomologous flanking sequences direct site specific integration into theplastome. Plastidal transformation has been described for many differentplant species and an overview is given in Bock (2001) Transgenicplastids in basic research and plant biotechnology. J Mol Biol. 2001Sep. 21; 312 (3):425-38 or Maliga, P (2003) Progress towardscommercialization of plastid transformation technology. TrendsBiotechnol. 21, 20-28. Further biotechnological progress has recentlybeen reported in form of marker free plastid transformants, which can beproduced by a transient co-integrated maker gene (Klaus et al., 2004,Nature Biotechnology 22(2), 225-229).

The genetically modified plant cells can be regenerated via all methodswith which the skilled worker is familiar. Suitable methods can be foundin the abovementioned publications by S. D. Kung and R. Wu, Potrykus orHöfgen and Willmitzer.

Generally after transformation, plant cells or cell groupings areselected for the presence of one or more markers which are encoded byplant-expressible genes co-transferred with the gene of interest,following which the transformed material is regenerated into a wholeplant. To select transformed plants, the plant material obtained in thetransformation is, as a rule, subjected to selective conditions so thattransformed plants can be distinguished from untransformed plants. Forexample, the seeds obtained in the above-described manner can be plantedand, after an initial growing period, subjected to a suitable selectionby spraying. A further possibility consists in growing the seeds, ifappropriate after sterilization, on agar plates using a suitableselection agent so that only the transformed seeds can grow into plants.Alternatively, the transformed plants are screened for the presence of aselectable marker such as the ones described above.

Following DNA transfer and regeneration, putatively transformed plantsmay also be evaluated, for instance using Southern analysis, for thepresence of the gene of interest, copy number and/or genomicorganisation. Alternatively or additionally, expression levels of thenewly introduced DNA may be monitored using Northern and/or Westernanalysis, both techniques being well known to persons having ordinaryskill in the art.

The generated transformed plants may be propagated by a variety ofmeans, such as by clonal propagation or classical breeding techniques.For example, a first generation (or T1) transformed plant may be selfedand homozygous second-generation (or T2) transformants selected, and theT2 plants may then further be propagated through classical breedingtechniques. The generated transformed organisms may take a variety offorms. For example, they may be chimeras of transformed cells andnon-transformed cells; clonal transformants (e.g., all cells transformedto contain the expression cassette); grafts of transformed anduntransformed tissues (e.g., in plants, a transformed rootstock graftedto an untransformed scion).

T-DNA Activation Tagging

T-DNA activation tagging (Hayashi et al. Science (1992) 1350-1353),involves insertion of T-DNA, usually containing a promoter (may also bea translation enhancer or an intron), in the genomic region of the geneof interest or 10 kb up- or downstream of the coding region of a gene ina configuration such that the promoter directs expression of thetargeted gene. Typically, regulation of expression of the targeted geneby its natural promoter is disrupted and the gene falls under thecontrol of the newly introduced promoter. The promoter is typicallyembedded in a T-DNA. This T-DNA is randomly inserted into the plantgenome, for example, through Agrobacterium infection and leads tomodified expression of genes near the inserted T-DNA. The resultingtransgenic plants show dominant phenotypes due to modified expression ofgenes close to the introduced promoter.

TILLING

The term “TILLING” is an abbreviation of “Targeted Induced Local LesionsIn Genomes” and refers to a mutagenesis technology useful to generateand/or identify nucleic acids encoding proteins with modified expressionand/or activity. TILLING also allows selection of plants carrying suchmutant variants. These mutant variants may exhibit modified expression,either in strength or in location or in timing (if the mutations affectthe promoter for example). These mutant variants may exhibit higheractivity than that exhibited by the gene in its natural form. TILLINGcombines high-density mutagenesis with high-throughput screeningmethods. The steps typically followed in TILLING are: (a) EMSmutagenesis (Redei G P and Koncz C (1992) In Methods in ArabidopsisResearch, Koncz C, Chua N H, Schell J, eds. Singapore, World ScientificPublishing Co, pp. 16-82; Feldmann et al., (1994) In Meyerowitz E M,Somerville C R, eds, Arabidopsis. Cold Spring Harbor Laboratory Press,Cold Spring Harbor, N.Y., pp 137-172; Lightner J and Caspar T (1998) InJ Martinez-Zapater, J Salinas, eds, Methods on Molecular Biology, Vol.82. Humana Press, Totowa, N.J., pp 91-104); (b) DNA preparation andpooling of individuals; (c) PCR amplification of a region of interest;(d) denaturation and annealing to allow formation of heteroduplexes; (e)DHPLC, where the presence of a heteroduplex in a pool is detected as anextra peak in the chromatogram; (f) identification of the mutantindividual; and (g) sequencing of the mutant PCR product. Methods forTILLING are well known in the art (McCallum et al., (2000) NatBiotechnol 18: 455-457; reviewed by Stemple (2004) Nat Rev Genet 5(2):145-50).

Homologous Recombination

Homologous recombination allows introduction in a genome of a selectednucleic acid at a defined selected position. Homologous recombination isa standard technology used routinely in biological sciences for lowerorganisms such as yeast or the moss Physcomitrella. Methods forperforming homologous recombination in plants have been described notonly for model plants (Offringa et al. (1990) EMBO J 9(10): 3077-84) butalso for crop plants, for example rice (Terada et al. (2002) Nat Biotech20(10): 1030-4; Iida and Terada (2004) Curr Opin Biotech 15(2): 132-8),and approaches exist that are generally applicable regardless of thetarget organism (Miller et al, Nature Biotechnol. 25, 778-785, 2007).

Yield Related Traits

Yield related traits are traits or features which are related to plantyield. Yield-related traits may comprise one or more of the followingnon-limitative list of features: early flowering time, yield, biomass,seed yield, early vigour, greenness index, increased growth rate,improved agronomic traits, such as e.g. improved Water Use Efficiency(WUE), improved Nitrogen Use Efficiency (NUE), etc.

Yield

The term “yield” in general means a measurable produce of economicvalue, typically related to a specified crop, to an area, and to aperiod of time. Individual plant parts directly contribute to yieldbased on their number, size and/or weight, or the actual yield is theyield per square meter for a crop and year, which is determined bydividing total production (includes both harvested and appraisedproduction) by planted square meters.

The terms “yield” of a plant and “plant yield” are used interchangeablyherein and are meant to refer to vegetative biomass such as root and/orshoot biomass, to reproductive organs, and/or to propagules such asseeds of that plant.

Taking corn as an example, male inflorescences (tassels) and femaleinflorescences (ears). The female inflorescence produces pairs ofspikelets on the surface of a central axis (cob). Each of the femalespikelets encloses two fertile florests, one of whose will usuallymature into a maize kernel once fertilized. Hence a yield increase inmaize may be manifested as one or more of the following: increase in thenumber of plants established per square meter, an increase in the numberof ears per plant, an increase in the number of rows, number of kernelsper row, kernel weight, thousand kernel weight, ear length/diameter,increase in the seed filling rate, which is the number of filled florets(i.e. florets containing seed) divided by the total number of floretsand multiplied by 100), among others.

Inflorescences in rice plants are called panicles. The panicle bearsspikelets. The spikelet is the basic unit of the panicles and consistsof a pedicel and a floret. The floret is born on the pedicel. A floretincludes a flower that is covered by two protective glumes: a largerglume (the lemma) and a shorter glume (the palea). Hence, taking rice asan example, a yield increase may manifest itself as an increase in oneor more of the following: number of plants per square meter, number ofpanicles per plant, panicle length, number of spikelets per panicle,number of flowers (or florets) per panicle, increase in the seed fillingrate which is the number of filled florets (i.e. florets containingseeds divided by the total number of floretsand multiplied by 100),increase in thousand kernel weight, among others. In rice, submergencetolerance may also result in increased yield.

Early Flowering Time

Plants having an “early flowering time” as used herein are plants whichstart to flower earlier than control plants. Hence this term refers toplants that show an earlier start of flowering. Flowering time of plantscan be assessed by counting the number of days (“time to flower”)between sowing and the emergence of a first inflorescence. The“flowering time” of a plant can for instance be determined using themethod as described in WO 2007/093444.

Early Vigour

“Early vigour” refers to active healthy well-balanced growth especiallyduring early stages of plant growth, and may result from increased plantfitness due to, for example, the plants being better adapted to theirenvironment (i.e. optimizing the use of energy resources andpartitioning between shoot and root). Plants having early vigour alsoshow increased seedling survival and a better establishment of the crop,which often results in highly uniform fields (with the crop growing inuniform manner, i.e. with the majority of plants reaching the variousstages of development at substantially the same time), and often betterand higher yield. Therefore, early vigour may be determined by measuringvarious factors, such as thousand kernel weight, percentage germination,percentage emergence, seedling growth, seedling height, root length,root and shoot biomass and many more.

Increased Growth Rate

The increased growth rate may be specific to one or more parts of aplant (including seeds), or may be throughout substantially the wholeplant. Plants having an increased growth rate may have a shorter lifecycle. The life cycle of a plant may be taken to mean the time needed togrow from a dry mature seed up to the stage where the plant has produceddry mature seeds, similar to the starting material. This life cycle maybe influenced by factors such as speed of germination, early vigour,growth rate, greenness index, flowering time and speed of seedmaturation. The increase in growth rate may take place at one or morestages in the life cycle of a plant or during substantially the wholeplant life cycle. Increased growth rate during the early stages in thelife cycle of a plant may reflect enhanced vigour. The increase ingrowth rate may alter the harvest cycle of a plant allowing plants to besown later and/or harvested sooner than would otherwise be possible (asimilar effect may be obtained with earlier flowering time). If thegrowth rate is sufficiently increased, it may allow for the furthersowing of seeds of the same plant species (for example sowing andharvesting of rice plants followed by sowing and harvesting of furtherrice plants all within one conventional growing period). Similarly, ifthe growth rate is sufficiently increased, it may allow for the furthersowing of seeds of different plants species (for example the sowing andharvesting of corn plants followed by, for example, the sowing andoptional harvesting of soybean, potato or any other suitable plant).Harvesting additional times from the same rootstock in the case of somecrop plants may also be possible. Altering the harvest cycle of a plantmay lead to an increase in annual biomass production per square meter(due to an increase in the number of times (say in a year) that anyparticular plant may be grown and harvested). An increase in growth ratemay also allow for the cultivation of transgenic plants in a widergeographical area than their wild-type counterparts, since theterritorial limitations for growing a crop are often determined byadverse environmental conditions either at the time of planting (earlyseason) or at the time of harvesting (late season). Such adverseconditions may be avoided if the harvest cycle is shortened. The growthrate may be determined by deriving various parameters from growthcurves, such parameters may be: T-Mid (the time taken for plants toreach 50% of their maximal size) and T-90 (time taken for plants toreach 90% of their maximal size), amongst others.

Stress Resistance

An increase in yield and/or growth rate occurs whether the plant isunder non-stress conditions or whether the plant is exposed to variousstresses compared to control plants. Plants typically respond toexposure to stress by growing more slowly. In conditions of severestress, the plant may even stop growing altogether. Mild stress on theother hand is defined herein as being any stress to which a plant isexposed which does not result in the plant ceasing to grow altogetherwithout the capacity to resume growth. Mild stress in the sense of theinvention leads to a reduction in the growth of the stressed plants ofless than 40%, 35%, 30% or 25%, more preferably less than 20% or 15% incomparison to the control plant under non-stress conditions. Due toadvances in agricultural practices (irrigation, fertilization, pesticidetreatments) severe stresses are not often encountered in cultivated cropplants. As a consequence, the compromised growth induced by mild stressis often an undesirable feature for agriculture. “Mild stresses” are theeveryday biotic and/or abiotic (environmental) stresses to which a plantis exposed. Abiotic stresses may be due to drought or excess water,anaerobic stress, salt stress, chemical toxicity, oxidative stress andhot, cold or freezing temperatures.

“Biotic stresses” are typically those stresses caused by pathogens, suchas bacteria, viruses, fungi, nematodes and insects.

The “abiotic stress” may be an osmotic stress caused by a water stress,e.g. due to drought, salt stress, or freezing stress. Abiotic stress mayalso be an oxidative stress or a cold stress. “Freezing stress” isintended to refer to stress due to freezing temperatures, i.e.temperatures at which available water molecules freeze and turn intoice. “Cold stress”, also called “chilling stress”, is intended to referto cold temperatures, e.g. temperatures below 10°, or preferably below5° C., but at which water molecules do not freeze. As reported in Wanget al. (Planta (2003) 218: 1-14), abiotic stress leads to a series ofmorphological, physiological, biochemical and molecular changes thatadversely affect plant growth and productivity. Drought, salinity,extreme temperatures and oxidative stress are known to be interconnectedand may induce growth and cellular damage through similar mechanisms.Rabbani et al. (Plant Physiol (2003) 133: 1755-1767) describes aparticularly high degree of “cross talk” between drought stress andhigh-salinity stress. For example, drought and/or salinisation aremanifested primarily as osmotic stress, resulting in the disruption ofhomeostasis and ion distribution in the cell. Oxidative stress, whichfrequently accompanies high or low temperature, salinity or droughtstress, may cause denaturing of functional and structural proteins. As aconsequence, these diverse environmental stresses often activate similarcell signaling pathways and cellular responses, such as the productionof stress proteins, up-regulation of anti-oxidants, accumulation ofcompatible solutes and growth arrest. The term “non-stress” conditionsas used herein are those environmental conditions that allow optimalgrowth of plants. Persons skilled in the art are aware of normal soilconditions and climatic conditions for a given location. Plants withoptimal growth conditions, (grown under non-stress conditions) typicallyyield in increasing order of preference at least 97%, 95%, 92%, 90%,87%, 85%, 83%, 80%, 77% or 75% of the average production of such plantin a given environment. Average production may be calculated on harvestand/or season basis. Persons skilled in the art are aware of averageyield productions of a crop.

In particular, the methods of the present invention may be performedunder non-stress conditions. In an example, the methods of the presentinvention may be performed under non-stress conditions such as milddrought to give plants having increased yield relative to controlplants.

In another embodiment, the methods of the present invention may beperformed under stress conditions.

In an example, the methods of the present invention may be performedunder stress conditions such as drought to give plants having increasedyield relative to control plants.

In another example, the methods of the present invention may beperformed under stress conditions such as nutrient deficiency to giveplants having increased yield relative to control plants.

Nutrient deficiency may result from a lack of nutrients such asnitrogen, phosphates and other phosphorous-containing compounds,potassium, calcium, magnesium, manganese, iron and boron, amongstothers.

In yet another example, the methods of the present invention may beperformed under stress conditions such as salt stress to give plantshaving increased yield relative to control plants. The term salt stressis not restricted to common salt (NaCl), but may be any one or more of:NaCl, KCl, LiCl, MgCl₂, CaCl₂, amongst others.

In yet another example, the methods of the present invention may beperformed under stress conditions such as cold stress or freezing stressto give plants having increased yield relative to control plants.

Increase/Improve/Enhance

The terms “increase”, “improve” or “enhance” are interchangeable andshall mean in the sense of the application at least a 3%, 4%, 5%, 6%,7%, 8%, 9% or 10%, preferably at least 15% or 20%, more preferably 25%,30%, 35% or 40% more yield and/or growth in comparison to control plantsas defined herein.

Seed Yield

Increased seed yield may manifest itself as one or more of thefollowing:

-   -   (a) an increase in seed biomass (total seed weight) which may be        on an individual seed basis and/or per plant and/or per square        meter;    -   (b) increased number of flowers per plant;    -   (c) increased number of seeds;    -   (d) increased seed filling rate (which is expressed as the ratio        between the number of filled florets divided by the total number        of florets);    -   (e) increased harvest index, which is expressed as a ratio of        the yield of harvestable parts, such as seeds, divided by the        biomass of aboveground plant parts; and    -   (f) increased thousand kernel weight (TKW), which is        extrapolated from the number of seeds counted and their total        weight. An increased TKW may result from an increased seed size        and/or seed weight, and may also result from an increase in        embryo and/or endosperm size.

An increase in seed yield may also be manifested as an increase in seedsize and/or seed volume. Furthermore, an increase in seed yield may alsomanifest itself as an increase in seed area and/or seed length and/orseed width and/or seed perimeter.

Greenness Index

The “greenness index” as used herein is calculated from digital imagesof plants. For each pixel belonging to the plant object on the image,the ratio of the green value versus the red value (in the RGB model forencoding color) is calculated. The greenness index is expressed as thepercentage of pixels for which the green-to-red ratio exceeds a giventhreshold. Under normal growth conditions, under salt stress growthconditions, and under reduced nutrient availability growth conditions,the greenness index of plants is measured in the last imaging beforeflowering. In contrast, under drought stress growth conditions, thegreenness index of plants is measured in the first imaging afterdrought.

Biomass

The term “biomass” as used herein is intended to refer to the totalweight of a plant. Within the definition of biomass, a distinction maybe made between the biomass of one or more parts of a plant, which mayinclude any one or more of the following:

-   -   aboveground parts such as but not limited to shoot biomass, seed        biomass, leaf biomass, etc.;    -   aboveground harvestable parts such as but not limited to shoot        biomass, seed biomass, leaf biomass, etc.:    -   parts below ground, such as but not limited to root biomass,        etc.;    -   harvestable parts below ground, such as but not limited to root        biomass, etc.;    -   vegetative biomass such as root biomass, shoot biomass, etc.,;    -   reproductive organs; and    -   propagules such as seed.

Marker Assisted Breeding

Such breeding programmes sometimes require introduction of allelicvariation by mutagenic treatment of the plants, using for example EMSmutagenesis; alternatively, the programme may start with a collection ofallelic variants of so called “natural” origin caused unintentionally.Identification of allelic variants then takes place, for example, byPCR. This is followed by a step for selection of superior allelicvariants of the sequence in question and which give increased yield.Selection is typically carried out by monitoring growth performance ofplants containing different allelic variants of the sequence inquestion. Growth performance may be monitored in a greenhouse or in thefield. Further optional steps include crossing plants in which thesuperior allelic variant was identified with another plant. This couldbe used, for example, to make a combination of interesting phenotypicfeatures.

Use as Probes in (Gene Mapping)

Use of nucleic acids encoding the protein of interest for geneticallyand physically mapping the genes requires only a nucleic acid sequenceof at least 15 nucleotides in length. These nucleic acids may be used asrestriction fragment length polymorphism (RFLP) markers. Southern blots(Sambrook J, Fritsch E F and Maniatis T (1989) Molecular Cloning, ALaboratory Manual) of restriction-digested plant genomic DNA may beprobed with the nucleic acids encoding the protein of interest. Theresulting banding patterns may then be subjected to genetic analysesusing computer programs such as MapMaker (Lander et al. (1987) Genomics1: 174-181) in order to construct a genetic map. In addition, thenucleic acids may be used to probe Southern blots containing restrictionendonuclease-treated genomic DNAs of a set of individuals representingparent and progeny of a defined genetic cross. Segregation of the DNApolymorphisms is noted and used to calculate the position of the nucleicacid encoding the protein of interest in the genetic map previouslyobtained using this population (Botstein et al. (1980) Am. J. Hum.Genet. 32:314-331).

The production and use of plant gene-derived probes for use in geneticmapping is described in Bernatzky and Tanksley (1986) Plant Mol. Biol.Reporter 4: 37-41. Numerous publications describe genetic mapping ofspecific cDNA clones using the methodology outlined above or variationsthereof. For example, F2 intercross populations, backcross populations,randomly mated populations, near isogenic lines, and other sets ofindividuals may be used for mapping. Such methodologies are well knownto those skilled in the art.

The nucleic acid probes may also be used for physical mapping (i.e.,placement of sequences on physical maps; see Hoheisel et al. In:Non-mammalian Genomic Analysis: A Practical Guide, Academic press 1996,pp. 319-346, and references cited therein).

In another embodiment, the nucleic acid probes may be used in directfluorescence in situ hybridisation (FISH) mapping (Trask (1991) TrendsGenet. 7:149-154). Although current methods of FISH mapping favour useof large clones (several kb to several hundred kb; see Laan et al.(1995) Genome Res. 5:13-20), improvements in sensitivity may allowperformance of FISH mapping using shorter probes.

A variety of nucleic acid amplification-based methods for genetic andphysical mapping may be carried out using the nucleic acids. Examplesinclude allele-specific amplification (Kazazian (1989) J. Lab. Clin. Med11:95-96), polymorphism of PCR-amplified fragments (CAPS; Sheffield etal. (1993) Genomics 16:325-332), allele-specific ligation (Landegren etal. (1988) Science 241:1077-1080), nucleotide extension reactions(Sokolov (1990) Nucleic Acid Res. 18:3671), Radiation Hybrid Mapping(Walter et al. (1997) Nat. Genet. 7:22-28) and Happy Mapping (Dear andCook (1989) Nucleic Acid Res. 17:6795-6807). For these methods, thesequence of a nucleic acid is used to design and produce primer pairsfor use in the amplification reaction or in primer extension reactions.The design of such primers is well known to those skilled in the art. Inmethods employing PCR-based genetic mapping, it may be necessary toidentify DNA sequence differences between the parents of the mappingcross in the region corresponding to the instant nucleic acid sequence.This, however, is generally not necessary for mapping methods.

Plant

The term “plant” as used herein encompasses whole plants, ancestors andprogeny of the plants and plant parts, including seeds, shoots, stems,leaves, roots (including tubers), flowers, and tissues and organs,wherein each of the aforementioned comprise the gene/nucleic acid ofinterest. The term “plant” also encompasses plant cells, suspensioncultures, callus tissue, embryos, meristematic regions, gametophytes,sporophytes, pollen and microspores, again wherein each of theaforementioned comprises the gene/nucleic acid of interest.

Plants that are particularly useful in the methods of the inventioninclude all plants which belong to the superfamily Viridiplantae, inparticular monocotyledonous and dicotyledonous plants including fodderor forage legumes, ornamental plants, food crops, trees or shrubsselected from the list comprising Acer spp., Actinidia spp., Abelmoschusspp., Agave sisalana, Agropyron spp., Agrostis stolonifera, Allium spp.,Amaranthus spp., Ammophila arenaria, Ananas comosus, Annona spp., Apiumgraveolens, Arachis spp, Artocarpus spp., Asparagus officinalis, Avenaspp. (e.g. Avena sativa, Avena fatua, Avena byzantina, Avena fatua var.sativa, Avena hybrida), Averrhoa carambola, Bambusa sp., Benincasahispida, Bertholletia excelsea, Beta vulgaris, Brassica spp. (e.g.Brassica napus, Brassica rapa ssp. [canola, oilseed rape, turnip rape]),Cadaba farinosa, Camellia sinensis, Canna indica, Cannabis sativa,Capsicum spp., Carex elata, Carica papaya, Carissa macrocarpa, Caryaspp., Carthamus tinctorius, Castanea spp., Ceiba pentandra, Cichoriumendivia, Cinnamomum spp., Citrullus lanatus, Citrus spp., Cocos spp.,Coffea spp., Colocasia esculenta, Cola spp., Corchorus sp., Coriandrumsativum, Corylus spp., Crataegus spp., Crocus sativus, Cucurbita spp.,Cucumis spp., Cynara spp., Daucus carota, Desmodium spp., Dimocarpuslongan, Dioscorea spp., Diospyros spp., Echinochloa spp., Elaeis (e.g.Elaeis guineensis, Elaeis oleifera), Eleusine coracana, Eragrostis tef,Erianthus sp., Eriobotrya japonica, Eucalyptus sp., Eugenia uniflora,Fagopyrum spp., Fagus spp., Festuca arundinacea, Ficus carica,Fortunella spp., Fragaria spp., Ginkgo biloba, Glycine spp. (e.g.Glycine max, Soja hispida or Soja max), Gossypium hirsutum, Helianthusspp. (e.g. Helianthus annuus), Hemerocallis fulva, Hibiscus spp.,Hordeum spp. (e.g. Hordeum vulgare), Ipomoea batatas, Juglans spp.,Lactuca sativa, Lathyrus spp., Lens culinaris, Linum usllatissimum,Litchi chinensis, Lotus spp., Luffa acutangula, Lupinus spp., Luzulasylvatica, Lycopersicon spp. (e.g. Lycopersicon esculentum, Lycopersiconlycopersicum, Lycopersicon pyriforme), Macrotyloma spp., Malus spp.,Malpighia emarginata, Mammea americana, Mangifera indica, Manihot spp.,Manilkara zapota, Medicago sativa, Melllotus spp., Mentha spp.,Miscanthus sinensis, Momordica spp., Morus nigra, Musa spp., Nicotianaspp., Olea spp., Opuntia spp., Ornithopus spp., Oryza spp. (e.g. Oryzasativa, Oryza latifolia), Panicum miliaceum, Panicum virgatum,Passiflora edulis, Pastinaca sativa, Pennisetum sp., Persea spp.,Petroselinum crispum, Phalaris arundinacea, Phaseolus spp., Phleumpratense, Phoenix spp., Phragmites australis, Physalis spp., Pinus spp.,Pistacia vera, Pisum spp., Poa spp., Populus spp., Prosopis spp., Prunusspp., Psidium spp., Punica granatum, Pyrus communis, Quercus spp.,Raphanus sativus, Rheum rhabarbarum, Ribes spp., Ricinus communis, Rubusspp., Saccharum spp., Salix sp., Sambucus spp., Secale cereale, Sesamumspp., Sinapis sp., Solanum spp. (e.g. Solanum tuberosum, Solanumintegrifolium or Solanum lycopersicum), Sorghum bicolor, Spinacia spp.,Syzygium spp., Tagetes spp., Tamarindus indica, Theobroma cacao,Trifolium spp., Tripsacum dactyloides, Triticosecale rimpaui, Triticumspp. (e.g. Triticum aestivum, Triticum durum, Triticum turgidum,Triticum hybernum, Triticum macha, Triticum sativum, Triticum monococcumor Triticum vulgare), Tropaeolum minus, Tropaeolum majus, Vacciniumspp., Vicia spp., Vigna spp., Viola odorata, Vitis spp., Zea mays,Zizania palustris, Ziziphus spp., amongst others.

Control Plant(s)

The choice of suitable control plants is a routine part of anexperimental setup and may include corresponding wild type plants orcorresponding plants without the gene of interest. The control plant istypically of the same plant species or even of the same variety as theplant to be assessed. The control plant may also be a nullizygote of theplant to be assessed. Nullizygotes are individuals missing the transgeneby segregation. A “control plant” as used herein refers not only towhole plants, but also to plant parts, including seeds and seed parts.

DETAILED DESCRIPTION OF THE INVENTION

Surprisingly, it has now been found that modulating expression in aplant of a nucleic acid encoding an SGT1 polypeptide gives plants havingenhanced yield-related traits relative to control plants. According to afirst embodiment, the present invention provides a method for enhancingyield-related traits in plants relative to control plants, comprisingmodulating expression in a plant of a nucleic acid encoding an SGT1polypeptide and optionally selecting for plants having enhancedyield-related traits.

The invention also provides hitherto unknown SGT1-encoding nucleic acidsand SGT1 polypeptides useful for conferring enhanced yield-relatedtraits in plants relative to control plants.

Furthermore, it has now surprisingly been found that modulatingexpression in a plant of a nucleic acid encoding a CLC-pKG polypeptidegives plants having enhanced yield-related traits relative to controlplants. According to a first embodiment, the present invention providesa method for enhancing yield-related traits in plants relative tocontrol plants, comprising modulating expression in a plant of a nucleicacid encoding a CLC-pKG polypeptide and optionally selecting for plantshaving enhanced yield-related traits.

Furthermore, it has now surprisingly been found that modulatingexpression in a plant of a nucleic acid encoding a HD-hydrolase-likepolypeptide gives plants having enhanced yield-related traits relativeto control plants. According to a first embodiment, the presentinvention provides a method for enhancing yield-related traits in plantsrelative to control plants, comprising modulating expression in a plantof a nucleic acid encoding a HD-hydrolase-like polypeptide andoptionally selecting for plants having enhanced yield-related traits.

A preferred method for modulating (preferably, increasing) expression ofa nucleic acid encoding an SGT1 polypeptide, or a CLC-pKG polypeptide,or a HD-hydrolase-like polypeptide, is by introducing and expressing ina plant a nucleic acid encoding an SGT1 polypeptide, or a CLC-pKGpolypeptide, or a HD-hydrolase-like polypeptide respectively.

In one embodiment a “protein useful in the methods of the invention” istaken to mean an SGT1 polypeptide as defined herein. Any referencehereinafter to a “nucleic acid useful in the methods of the invention”is taken to mean a nucleic acid capable of encoding such an SGT1polypeptide. The nucleic acid to be introduced into a plant (andtherefore useful in performing the methods of the invention) is anynucleic acid encoding the type of protein which will now be described,hereinafter also named “SGT1 nucleic acid” or “SGT1 gene”.

An “SGT1 polypeptide” as defined herein refers to any polypeptidecomprising the following in any order:

-   -   1. at least one tetratricopeptide (TPR) repeat;    -   2. at least one CS domain; and    -   3. an SGS domain.

The TPR is a structural motif involved in the mediation ofprotein-protein interactions and the assembly of multiprotein complexes.PFam Accession number PF00515 represents TPRs. See also InterproAccession number IPR001440 for further information on TPRs. SGT1polypeptides useful in the methods of the invention comprise at leastone TPR, preferably two TPRs and most preferably three TPRs.

The first TPR is a Type 1 TPR (TPR1) and is represented by the sequencegiven below or by a sequence having in increasing order of preference atleast 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%,83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,97%, 98%, or 99% or more sequence identity to the sequence of TPR1.

TPR1: (SEQ ID NO: 37) SKAYLRKGLACMKLEEYQTAKAALETGASLAPGE

The second TPR is a Type 2 TPR (TPR2) and is represented by the sequencegiven below or by a sequence having in increasing order of preference atleast 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%,83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,97%, 98%, or 99% or more sequence identity to the sequence of TPR2a.

TPR2a: (SEQ ID NO: 38) ASDLETRAKEAFIDDHFELAVDLYTQAISLSPKN

The third TPR is also a Type 2 TPR (TPR2) is represented by the sequencegiven below or by a sequence having in increasing order of preference atleast 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%,83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,97%, 98%, or 99% or more sequence identity to the sequence of TPR2b.

TPR2b: (SEQ ID NO: 39) PELFADRAQANIKLNYFTEAVVDANKAIELDPYM

PFam Accession number PF04969 represents CS domains. See also InterproAccession number IPR017447 for further information on CS domains. The CSdomain is represented by the sequence below or by a sequence having inincreasing order of preference at least 70%, 71%, 72%, 73%, 74%, 75%,76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%,90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% or more sequenceidentity to the sequence below.

CS Domain:

(SEQ ID NO: 40) YRHEFYQKPEEVVVTIFAKGIPAKNVVVDFGEQILSVSIDLPGGETYSFQPRLFGKITPAKCRYEVMSTKIEIRLAK

PFam Accession number PF05002 represents SGS domains. See also InterproAccession number IPR007699 for further information on SGS domains. TheSGS domain is represented by the sequence below or by a sequence havingin increasing order of preference at least 70%, 71%, 72%, 73%, 74%, 75%,76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%,90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% or more sequenceidentity to the sequence below.

SGS Domain:

(SEQ ID NO: 41) NVDWDKLEAQVKKEEKDEKLDGDAALNKFFRDIYKDADEDTRRAMMKSFVESNGTVLSTNWKKVGTKKVEGSPPDGMELKKW

According to a preferred feature of the present invention, SGT1polypeptides useful in the methods of the invention may comprise any oneor more of Motifs 1 to 8 as defined below:

Motif 1: DLETRAKEAFIDDHFELAVDLYTQAI, or a sequence having in increasingorder of preference at least 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%,78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%,92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% or more sequence identity tothe sequence of Motif 1 (SEQ ID NO: 42).

Motif 2: ADRAQANIKL, or a sequence having in increasing order ofpreference at least 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%,80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%,94%, 95%, 96%, 97%, 98%, or 99% or more sequence identity to thesequence of Motif 2 (SEQ ID NO: 43).

Motif 3: LEEYQTAKAALETGAS, or a sequence having in increasing order ofpreference at least 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%,80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%,94%, 95%, 96%, 97%, 98%, or 99% or more sequence identity to thesequence of Motif 3 (SEQ ID NO: 44).

Motif 4: KYRHEFYQKPEEVVVTIFAKGIP, or a sequence having in increasingorder of preference at least 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%,78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%,92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% or more sequence identity tothe sequence of Motif 4 (SEQ ID NO: 45).

Motif 5: QPRLFGKITPAKCRYEVMSTKIEIRLAKAE, or a sequence having inincreasing order of preference at least 70%, 71%, 72%, 73%, 74%, 75%,76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%,90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% or more sequenceidentity to the sequence of Motif 5 (SEQ ID NO: 46).

Motif 6: EAQVKKEEKDEKLDGDA, or a sequence having in increasing order ofpreference at least 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%,80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%,94%, 95%, 96%, 97%, 98%, or 99% or more sequence identity to thesequence of Motif 6 (SEQ ID NO: 47).

Motif 7: ALNKFFRDIYKDADEDTRRAMMKSFVESNGTVLSTNWKKVGTKKVEG, or a sequencehaving in increasing order of preference at least 70%, 71%, 72%, 73%,74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%,88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% or moresequence identity to the sequence of Motif 7 (SEQ ID NO: 48).

Motif 8: SPPDGMELKKWEI, or a sequence having in increasing order ofpreference at least 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%,80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%,94%, 95%, 96%, 97%, 98%, or 99% or more sequence identity to thesequence of Motif 8 (SEQ ID NO: 49).

Preferably, the SGT1 polypeptide comprises in increasing order ofpreference, at least 2, at least 3, at least 4, at least 5, at least 6,at least 7 or all 8 of the motifs as defined above.

Additionally, SGT1 polypeptides typically have in increasing order ofpreference at least 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%,35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%,49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%,63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%,77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%,91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% overall sequence identityto the amino acid represented by SEQ ID NO: 2.

The overall sequence identity is determined using a global alignmentalgorithm, such as the Needleman Wunsch algorithm in the program GAP(GCG Wisconsin Package, Accelrys), preferably with default parametersand preferably with sequences of mature proteins (i.e. without takinginto account secretion signals or transit peptides).

Compared to overall sequence identity, the sequence identity willgenerally be higher when only conserved domains or motifs areconsidered.

Preferably, the polypeptide sequence which when used in the constructionof a phylogenetic tree, such as the one depicted in FIG. 2, clusterswith the group of SGT1 polypeptides comprising the amino acid sequencerepresented by SEQ ID NO: 2 rather than with any other group.

In another embodiment a “protein useful in the methods of the invention”is taken to mean a CLC-pKG polypeptide as defined herein. Any referencehereinafter to a “nucleic acid useful in the methods of the invention”is taken to mean a nucleic acid capable of encoding such a CLC-pKGpolypeptide. The nucleic acid to be introduced into a plant (andtherefore useful in performing the methods of the invention) is anynucleic acid encoding the type of protein which will now be described,hereafter also named “CLC-pKG nucleic acid” or “CLC-pKG gene”.

A “CLC-pKG polypeptide” as defined herein refers to any polypeptidecomprising a Voltage CLC domain (Pfam entry PF00654) and C-terminallythereof a CBS domain (Pfam entry PF00571; Interpro entry IPR000644) andoptionally a USP domain (Pfam entry PF00582; Interpro entry IPR006016).CLC-pKG polypeptides are part of a family of voltage-gated channels thatis highly conserved over various kingdoms of life and are structurallyunrelated to the other known voltage-gated channels. They are found inorganisms ranging from bacteria to yeasts and plants, and also inanimals. CLC-pKG polypeptides typically have 10 or 12 transmembrane (TM)domains, occasionally less than 10 TM domains or more than 12, up to 18or 20 TM domains may occur. The CLC-pKG polypeptide represented by theArabidopsis AtCLCe and AtCLCf proteins show up to 12 membrane-spanningdomains Marmagne el al. 2007. CBS (cystathionine-beta-synthase) domainsare small intracellular modules, mostly found in two or four copieswithin a protein (two copies for CLC-pKG proteins), and are present inseveral different proteins in all kingdoms of life. Tandem pairs of CBSdomains, also called Baeteman domains, can act as binding domains foradenosine derivatives and may regulate the activity of attachedenzymatic or other domains. Typically CBS domains in CLC-pKGpolypeptides are proposed to play a role as a sensor for the energystatus of the cell. USP (Universal Stress Protein) domains are conservedprotein regions present in proteins whose expression in nature istypically enhanced when the cell is exposed to stress agents. It wasfirst characterized in the universal stress protein UspA (Nystrom T,Neidhardt F C. Mol. Microbiol. 11 537-44 1994), which is proposed tohave a a general “stress endurance” activity in E. coli.

Preferably, the CLC-pKG polypeptide useful in the methods of the presentinventions comprises a domain having in increasing order of preferenceat least 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%,37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%,51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%,65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%,79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%,93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to:

-   -   (i) a CLC in SEQ ID NO: 54 as represented by the sequence        located between amino acids 77 and 422 of SEQ ID NO: 54;    -   (ii) a CBS domain in SEQ ID NO: 54 as represented by the        sequence located between amino acids 455 to 510 or 516 to 571 of        SEQ ID NO: 54; and optionally    -   (iii) a USP domain in SEQ ID NO: 54 as represented by the        sequence located between amino acids 597-731 of SEQ ID NO: 54.

Preferably, the CLC-pKG polypeptide useful in the methods of the presentinventions comprises one or more of motifs 9 or 10:

(i) Motif 9: (SEQ ID NO: 113) P(T/S)(V/I)(H/Q)(I/V)GA(A/S/G)LA;(ii) Motif 10: (SEQ ID NO: 114)(P/S)GG(I/L/V)(F/L)XP(A/S/T)LX(L/M)G(S/A/T)XLG;

Wherein up to one, two, three, four, five, six, seven amino acids may besubstituted by any amino acid preferably by a semiconservative aminoacid more preferably by a conservative amino acid.

Additionally or alternatively, the CLC-pKG polypeptide useful in themethods of the invention or a homologue thereof has in increasing orderof preference at least 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%,35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%,49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%,63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%,77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%,91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% overall sequenceidentity to the amino acid represented by any one of the polypeptides ofTable A2, preferably by SEQ ID NO: 54, provided that the polypeptidecomprises the conserved domains as outlined above.

The overall sequence identity is determined using a global alignmentalgorithm, such as the Needleman Wunsch algorithm in the program GAP(GCG Wisconsin Package, Accelrys), preferably with default parametersand preferably with sequences of mature proteins (i.e. without takinginto account secretion signals or transit peptides). Compared to overallsequence identity, the sequence identity will generally be higher whenonly conserved domains or motifs are considered.

In a preferred embodiment the CLC-pKG nucleic acid and/or polypeptideuseful in the methods of the invention is of natural origin, more ofplant origin, most preferably of prokaryotic origin. Preferred plantCLC-pKG polypeptides are AtClC-e (At4g35440) and AtClC-f (At1g55620) asdescribed by Marmagne et al 2007 and having the locus number or SpinachCLCf as described by Teardo et al. 2005 FEBS Letters 579 (2005)4991-4996. As described by Teardo et al. 2005, AtClC-f and AtClC-e areclose related in sequence structure to cyanobacterial ClC channels (SeeTable 1 of Teardo et al. 2005). In particular the similarity with thethe Synechocystis sp. PCC 6803 protein, sll1864, the sequence similarityis of 20% with AtClC-e and of 21% with AtClC-f. Preferred prokaryoticCLC-pKG polypeptides are the polypeptides of Synechocystis species, morepreferably of Synechocystis sp. PCC 6803, most preferably polypeptidesll1864 of Synechocystis sp. PCC 6803, herein provided under SEQ ID NO:54.

Alternatively or additonaly, the CLC-pKG polypeptide sequence useful inthe methods of the invention when used in the construction of aphylogenetic tree, such as the one depicted in FIG. 1 of Marmagne et al.2007 (herein incorporated by reference), clusters with the group of CLCpolypeptides of bacterial origin, preferably with SCLC (P74477) fromSynechocystis sp.; or with the group of plant origin comprising AtCLCeand AtCLCf than with any other anion group. FIG. 1 of Marmagne et al.2007 is given in FIG. 6 herein.

Furthermore, CLC-like polypeptides (at least in their native form)typically have nitrate/H⁺ exchanging activity. Tools and techniques formeasuring anion transporting activity are well known in the art, forexample by complementation of yeast mutants (Marmagne et al., J. Exp.Bot. 58, 3385-3393, 2007) or complementation of Arabidopsis mutants (DeAngeli, 2009). Further details are provided in the Example section.

Selectivity of CLC chloride channels for different anions vary amongstclasses of CLC proteins. Thus AtCLCa of Arabidopsis thaliana, closer toCLC proteins of eukaryotic origin (see FIG. 6) was shown to have ahigher selectivity for NO3- anions than for Chloride, Cl—.

A further preferred CLC-pKG polypeptide useful in the methods of theinvention has a higher selectivity for Chloride than for Nitrate anions.

Plant CLC polypeptides are localized to membranes, with differentclasses of CLC localized to different membranes, for example to theplasma, the tonoplast, the chloroplast or the golgi membranes. A yetfurther preferred CLC-pKG polypeptide useful in the methods of theinvention localizes to the Golgi or to the Thylakoid membranes whenexpressed in a plant cell.

In addition or alternatively, CLC-pKG polypeptides, when expressed inrice according to the methods of the present invention as outlined inthe Examples section herein give plants having increased yield relatedtraits in comparison to control plants, in particular an increase in anyone or more of seed yield, harvest index, height of the plant, leafbiomass when grown under non-stress conditions.

In yet another embodiment a “protein useful in the methods of theinvention” is taken to mean a HD-hydrolase-like polypeptide as definedherein. Any reference hereinafter to a “nucleic acid useful in themethods of the invention” is taken to mean a nucleic acid capable ofencoding such a HD-hydrolase-like polypeptide. The nucleic acid to beintroduced into a plant (and therefore useful in performing the methodsof the invention) is any nucleic acid encoding the type of protein whichwill now be described, hereafter also named “HD-hydrolase-like nucleicacid” or “HD-hydrolase-like gene”.

A “HD-hydrolase-like polypeptide” as defined herein refers to a proteincomprising the CRISPR-associated protein Crm2 domain (InterPro accessionIPR013407). Preferably the HD-hydrolase-like protein comprises one ormore of the following motifs:

Motif 11 (SEQ ID NO: 148): (A/G/S/Q)(R/Y/F/L)(L/F/N)H(D/S)(P/S)(A/P/L)Preferably, motif 11 is (G/A)LLHDPA Motif 12 (SEQ ID NO: 149):P(A/Q)(D/E/H)(T/Y/S)(R/I)(I/F/A/L)P(D/N)Preferably, motif 12 is PA(D/E)TR(I/F/A/L)P(D/N)Motif 13 (SEQ ID NO: 150): (T/S)(L/I/F)(G/S/N)P(V/I)Q(E/S/Q/D/R)(L/F/Y)IPreferably, motif 13 is (T/S)(L/I/F)(G/S)P(V/I)Q (E/S)(L/F/Y)IMotif 14 (SEQ ID NO: 151):D(L/F)(W/Y/F)(A/W/M/T)(G/S)S(H/Y/W/F/M)(L/I/M)L (A/S/H)(R/Y/D)(L/F).Preferably, motif 14 is D(L/F)(W/Y/F)(A/W/M/T)GS(H/Y/W)(L/I/M)L(A/S/H)(R/Y)(L/F) Motif 15 (SEQ ID NO: 152):(L/I/V)(F/Y/T)PXL Wherein X can be any amino acid but preferablyone of Q, R, E, N, S, C or D Motif 16 (SEQ ID NO: 153):(L/M/F/I)PN(R/V/T)(F/I/L) Motif 17 (SEQ ID NO: 154): (M/L/G/F)DGDX(M/I)Wherein X can be any amino acid but preferablyone of R, Y, N, H, G, S or D Preferably, motif 7 is GDGD(G/S/D)MMotif 18 SEQ ID NO: 155): (S/T/G/A)P(A/G/S/T)(R/V/L/T/I)H(L/S/Q/N/V/A)(A/L/T/G/F)(I/L/V) (S/N) (G/E/R/L) Motif 19 (SEQ ID NO: 156):G(R/K)(V/L)(L/I/V)Y(A/S)GGDD(L/V)(M/F/L)(A/T) Motif 20 (SEQ ID NO: 157):(T/S)(A/M/I/L)S(M/A/F/C/L)G(A/V/I/L)(V/T/A)I (A/V/G)(H/D)(H/Y/K)(K/Q/S)

Additionally or alternatively, the HD-hydrolase-like polypeptidecomprises one or more of the following motifs:

Motif 21 (SEQ ID NO: 158): IKASRK(F/I/M)(L/R/K)DFWAGS(Y/W)(L/I)LHYLSAMotif 22 (SEQ ID NO: 159): L(A/L)TAGFPN Motif 23 (SEQ ID NO: 160):GLFDG(S/T/R/I)E(M/K/Q)LNA(L/T)E(L/I/T)(T/V/L)KRMotif 24 (SEQ ID NO: 161): KRMGP(A/S)TH(V/S/N)(G/A)L(N/S)RALLDFSMotif 25 (SEQ ID NO: 162): Y(S/A)GGDDV Motif 26 (SEQ ID NO: 163):LFT(M/L)G(F/K/S/Q/D)(G/C/L/A/N)A(T/S)(M/I)S(L/F)G(I/V/L)(V/T)I(V/A)(D/H)(K/H)S(V/I)PL(P/A)(V/I) ALE(A/S/N)LW(E/Q)AE

More preferably, the HD-hydrolase-like polypeptide comprises inincreasing order of preference, at least 2, at least 3, at least 4, atleast 5, at least 6, at least 7, at least 8, at least 9, at least 10, atleast 11, at least 12, at least 13, at least 14, at least 15, or all 16motifs.

Additionally or alternatively, the homologue of a HD-hydrolase-likeprotein has in increasing order of preference at least 25%, 26%, 27%,28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%,42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%,56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%,70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%,84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%,98%, or 99% overall sequence identity to the amino acid represented bySEQ ID NO: 119, provided that the homologous protein comprises any oneor more of the conserved motifs as outlined above. The overall sequenceidentity is determined using a global alignment algorithm, such as theNeedleman Wunsch algorithm in the program GAP (GCG Wisconsin Package,Accelrys), preferably with default parameters and preferably withsequences of mature proteins (i.e. without taking into account secretionsignals or transit peptides). Compared to overall sequence identity, thesequence identity will generally be higher when only conserved domainsor motifs are considered. Preferably the motifs in a HD-hydrolase-likepolypeptide have, in increasing order of preference, at least 70%, 71%,72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%,86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%sequence identity to any one or more of the motifs represented by SEQ IDNO: 148 to SEQ ID NO: 163 (Motifs 11 to 26).

Preferably, the polypeptide sequence which when used in the constructionof a phylogenetic tree, such as the one depicted in FIG. 10, clusterswith the group of HD-hydrolase-like polypeptides comprising the aminoacid sequence represented by SEQ ID NO: 119 rather than with any othergroup.

HD-hydrolase-like polypeptides, when expressed in rice according to themethods of the present invention as outlined in Examples 6 and 7, giveplants having increased yield related traits, such as increased seedyield.

The terms “domain”, “signature” and “motif” are defined in the“definitions” section herein.

Concerning SGT1 polypeptides, the present invention is illustrated bytransforming plants with the nucleic acid sequence represented by SEQ IDNO: 1, encoding the polypeptide sequence of SEQ ID NO: 2. However,performance of the invention is not restricted to these sequences; themethods of the invention may advantageously be performed using anySGT1-encoding nucleic acid or SGT1 polypeptide as defined herein.

Examples of nucleic acids encoding SGT1 polypeptides are given in TableA1 of the Examples section herein. Such nucleic acids are useful inperforming the methods of the invention. The amino acid sequences givenin Table A1 of the Examples section are example sequences of orthologuesand paralogues of the SGT1 polypeptide represented by SEQ ID NO: 2, theterms “orthologues” and “paralogues” being as defined herein. Furtherorthologues and paralogues may readily be identified by performing aso-called reciprocal blast search as described in the definitionssection; where the query sequence is SEQ ID NO: 1 or SEQ ID NO: 2, thesecond BLAST (back-BLAST) would be against Capsicum sequences.

Concerning CLC-pKG polypeptides, the present invention is illustrated bytransforming plants with the nucleic acid sequence represented by SEQ IDNO: 53, encoding the polypeptide sequence of SEQ ID NO: 54. However,performance of the invention is not restricted to these sequences; themethods of the invention may advantageously be performed using anyCLC-pKG-encoding nucleic acid or CLC-pKG polypeptide as defined herein.

Examples of nucleic acids encoding CLC-pKG polypeptides are given inTable A2 of the Examples section herein. Such nucleic acids are usefulin performing the methods of the invention. The amino acid sequencesgiven in Table A2 of the Examples section are example sequences oforthologues and paralogues of the CLC-pKG polypeptide represented by SEQID NO: 54, the terms “orthologues” and “paralogues” being as definedherein. Further orthologues and paralogues may readily be identified byperforming a so-called reciprocal blast search as described in thedefinitions section; where the query sequence is SEQ ID NO: 53 or SEQ IDNO: 54, the second BLAST (back-BLAST) would be against rice sequences.

Concerning HD-hydrolase-like polypeptides, the present invention isillustrated by transforming plants with the nucleic acid sequencerepresented by SEQ ID NO: 118, encoding the polypeptide sequence of SEQID NO: 119. However, performance of the invention is not restricted tothese sequences; the methods of the invention may advantageously beperformed using any HD-hydrolase-like-encoding nucleic acid orHD-hydrolase-like polypeptide as defined herein.

Examples of nucleic acids encoding HD-hydrolase-like polypeptides aregiven in Table A3 of the Examples section herein. Such nucleic acids areuseful in performing the methods of the invention. The amino acidsequences given in Table A3 of the Examples section are examplesequences of orthologues and paralogues of the HD-hydrolase-likepolypeptide represented by SEQ ID NO: 119, the terms “orthologues” and“paralogues” being as defined herein. Further orthologues and paraloguesmay readily be identified by performing a so-called reciprocal blastsearch as described in the definitions section; where the query sequenceis SEQ ID NO: 118 or SEQ ID NO: 119, the second BLAST (back-BLAST) wouldbe against Synechocystis sequences.

Nucleic acid variants may also be useful in practising the methods ofthe invention. Examples of such variants include nucleic acids encodinghomologues and derivatives of any one of the amino acid sequences givenin Table A1 to A3 of the Examples section, the terms “homologue” and“derivative” being as defined herein. Also useful in the methods of theinvention are nucleic acids encoding homologues and derivatives oforthologues or paralogues of any one of the amino acid sequences givenin Table A1 to A3 of the Examples section. Homologues and derivativesuseful in the methods of the present invention have substantially thesame biological and functional activity as the unmodified protein fromwhich they are derived. Further variants useful in practising themethods of the invention are variants in which codon usage is optimisedor in which miRNA target sites are removed.

Further nucleic acid variants useful in practising the methods of theinvention include portions of nucleic acids encoding SGT1 polypeptides,or CLC-pKG polypeptides, or HD-hydrolase-like polypeptides, nucleicacids hybridising to nucleic acids encoding SGT1 polypeptides, orCLC-pKG polypeptides, or HD-hydrolase-like polypeptides, splice variantsof nucleic acids encoding SGT1 polypeptides, or CLC-pKG polypeptides, orHD-hydrolase-like polypeptides, allelic variants of nucleic acidsencoding SGT1 polypeptides and variants of nucleic acids encoding SGT1polypeptides, or CLC-pKG polypeptides, or HD-hydrolase-likepolypeptides, obtained by gene shuffling. The terms hybridisingsequence, splice variant, allelic variant and gene shuffling are asdescribed herein.

Nucleic acids encoding SGT1 polypeptides, or CLC-pKG polypeptides, orHD-hydrolase-like polypeptides, need not be full-length nucleic acids,since performance of the methods of the invention does not rely on theuse of full-length nucleic acid sequences. According to the presentinvention, there is provided a method for enhancing yield-related traitsin plants, comprising introducing and expressing in a plant a portion ofany one of the nucleic acid sequences given in Table A1 to A3 of theExamples section, or a portion of a nucleic acid encoding an orthologue,paralogue or homologue of any of the amino acid sequences given in TableA1 to A3 of the Examples section.

A portion of a nucleic acid may be prepared, for example, by making oneor more deletions to the nucleic acid. The portions may be used inisolated form or they may be fused to other coding (or non-coding)sequences in order to, for example, produce a protein that combinesseveral activities. When fused to other coding sequences, the resultantpolypeptide produced upon translation may be bigger than that predictedfor the protein portion.

Concerning SGT1 polypeptides, portions useful in the methods of theinvention, encode a SGT1 polypeptide as defined herein, and havesubstantially the same biological activity as the amino acid sequencesgiven in Table A1 of the Examples section. Preferably, the portion is aportion of any one of the nucleic acids given in Table A1 of theExamples section, or is a portion of a nucleic acid encoding anorthologue or paralogue of any one of the amino acid sequences given inTable A1 of the Examples section. Preferably the portion is at least500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000 consecutivenucleotides in length, the consecutive nucleotides being of any one ofthe nucleic acid sequences given in Table A1 of the Examples section, orof a nucleic acid encoding an orthologue or paralogue of any one of theamino acid sequences given in Table A1 of the Examples section. Mostpreferably the portion is a portion of the nucleic acid of SEQ ID NO: 1.Preferably, the portion encodes a fragment of an amino acid sequencewhich, when used in the construction of a phylogenetic tree, clusterswith the group of SGT1 polypeptides comprising the amino acid sequencerepresented by SEQ ID NO: 2 rather than with any other.

Concerning CLC-pKG polypeptides, portions useful in the methods of theinvention, encode a CLC-pKG polypeptide as defined herein, and havesubstantially the same biological activity as the amino acid sequencesgiven in Table A2 of the Examples section. Preferably, the portion is aportion of any one of the nucleic acids given in Table A2 of theExamples section, or is a portion of a nucleic acid encoding anorthologue or paralogue of any one of the amino acid sequences given inTable A2 of the Examples section. Preferably the portion is at least100, 200, 300, 400, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950,1000 consecutive nucleotides in length, the consecutive nucleotidesbeing of any one of the nucleic acid sequences given in Table A2 of theExamples section, or of a nucleic acid encoding an orthologue orparalogue of any one of the amino acid sequences given in Table A2 ofthe Examples section. Most preferably the portion is a portion of thenucleic acid of SEQ ID NO: 53. Preferably, the portion encodes afragment of an amino acid sequence which, when used in the constructionof a phylogenetic tree, such as the one depicted in FIG. 1 of Marmagneet al. 2007 (herein incorporated by reference), clusters with the groupof CLC polypeptides of bacterial origin, preferably with SCLC (P74477)from Synechocystis sp.; or with the group of plant origin comprisingAtCLCe and AtCLCf than with any other anion group.

Concerning HD-hydrolase-like polypeptides, portions useful in themethods of the invention, encode a HD-hydrolase-like polypeptide asdefined herein, and have substantially the same biological activity asthe amino acid sequences given in Table A3 of the Examples section.Preferably, the portion is a portion of any one of the nucleic acidsgiven in Table A3 of the Examples section, or is a portion of a nucleicacid encoding an orthologue or paralogue of any one of the amino acidsequences given in Table A3 of the Examples section. Preferably theportion is at least 1000, 1100, 1200, 1300, 1400, 1500, 1600, 1700,1800, 1900, 2000, 2100, 2200, 2300, 2400, 2500, 2600, 2700, 2800, 2900,3000, 3100, 3200, 3300, 3400, 3500, 3600, 3700 consecutive nucleotidesin length, the consecutive nucleotides being of any one of the nucleicacid sequences given in Table A3 of the Examples section, or of anucleic acid encoding an orthologue or paralogue of any one of the aminoacid sequences given in Table A3 of the Examples section. Mostpreferably the portion is a portion of the nucleic acid of SEQ ID NO:118. Preferably, the portion encodes a fragment of an amino acidsequence which, when used in the construction of a phylogenetic tree,such as the one depicted in FIG. 10, clusters with the group ofHD-hydrolase-like polypeptides comprising the amino acid sequencerepresented by SEQ ID NO: 119 rather than with any other group and/orcomprises any one or more of the motifs 11 to 26 defined above.

Another nucleic acid variant useful in the methods of the invention is anucleic acid capable of hybridising, under reduced stringencyconditions, preferably under stringent conditions, with a nucleic acidencoding an SGT1 polypeptide, or a CLC-pKG polypeptide, or aHD-hydrolase-like polypeptide, as defined herein, or with a portion asdefined herein.

According to the present invention, there is provided a method forenhancing yield-related traits in plants, comprising introducing andexpressing in a plant a nucleic acid capable of hybridizing to any oneof the nucleic acids given in Table A1 to A3 of the Examples section, orcomprising introducing and expressing in a plant a nucleic acid capableof hybridising to a nucleic acid encoding an orthologue, paralogue orhomologue of any of the nucleic acid sequences given in Table A1 to A3of the Examples section.

Concerning SGT1 polypeptides, hybridising sequences useful in themethods of the invention encode an SGT1 polypeptide as defined herein,having substantially the same biological activity as the amino acidsequences given in Table A1 of the Examples section. Preferably, thehybridising sequence is capable of hybridising to the complement of anyone of the nucleic acids given in Table A1 of the Examples section, orto a portion of any of these sequences, a portion being as definedabove, or the hybridising sequence is capable of hybridising to thecomplement of a nucleic acid encoding an orthologue or paralogue of anyone of the amino acid sequences given in Table A1 of the Examplessection. Most preferably, the hybridising sequence is capable ofhybridising to the complement of a nucleic acid as represented by SEQ IDNO: 1 or to a portion thereof.

Preferably, the hybridising sequence encodes a polypeptide with an aminoacid sequence which, when substantially full-length and used in theconstruction of a phylogenetic tree, clusters with the group of SGT1polypeptides comprising the amino acid sequence represented by SEQ IDNO: 2 rather than with any other.

Concerning CLC-pKG polypeptides, hybridising sequences useful in themethods of the invention encode a CLC-pKG polypeptide as defined herein,having substantially the same biological activity as the amino acidsequences given in Table A2 of the Examples section. Preferably, thehybridising sequence is capable of hybridising to the complement of anyone of the nucleic acids given in Table A2 of the Examples section, orto a portion of any of these sequences, a portion being as definedabove, or the hybridising sequence is capable of hybridising to thecomplement of a nucleic acid encoding an orthologue or paralogue of anyone of the amino acid sequences given in Table A2 of the Examplessection. Most preferably, the hybridising sequence is capable ofhybridising to the complement of a nucleic acid as represented by SEQ IDNO: 53 or to a portion thereof.

Preferably, the hybridising sequence encodes a polypeptide with an aminoacid sequence which, when full-length and used in the construction of aphylogenetic tree, such as the one depicted in FIG. 1 of Marmagne et al.2007 (herein incorporated by reference), clusters with the group of CLCpolypeptides of bacterial origin, preferably with SCLC (P74477) fromSynechocystis sp.; or with the group of plant origin comprising AtCLCeand AtCLCf than with any other anion group.

Concerning HD-hydrolase-like polypeptides, hybridising sequences usefulin the methods of the invention encode a HD-hydrolase-like polypeptideas defined herein, having substantially the same biological activity asthe amino acid sequences given in Table A3 of the Examples section.Preferably, the hybridising sequence is capable of hybridising to thecomplement of any one of the nucleic acids given in Table A3 of theExamples section, or to a portion of any of these sequences, a portionbeing as defined above, or the hybridising sequence is capable ofhybridising to the complement of a nucleic acid encoding an orthologueor paralogue of any one of the amino acid sequences given in Table A3 ofthe Examples section. Most preferably, the hybridising sequence iscapable of hybridising to the complement of a nucleic acid asrepresented by SEQ ID NO: 118 or to a portion thereof.

Preferably, the hybridising sequence encodes a polypeptide with an aminoacid sequence which, when full-length and used in the construction of aphylogenetic tree, such as the one depicted in FIG. 10, clusters withthe group of HD-hydrolase-like polypeptides comprising the amino acidsequence represented by SEQ ID NO: 119 rather than with any other groupand/or comprises any one or more of the motifs 11 to 26 defined above.

Another nucleic acid variant useful in the methods of the invention is asplice variant encoding an SGT1 polypeptide, or a CLC-pKG polypeptide,or a HD-hydrolase-like polypeptide, as defined hereinabove, a splicevariant being as defined herein.

According to the present invention, there is provided a method forenhancing yield-related traits in plants, comprising introducing andexpressing in a plant a splice variant of any one of the nucleic acidsequences given in Table A1 to A3 of the Examples section, or a splicevariant of a nucleic acid encoding an orthologue, paralogue or homologueof any of the amino acid sequences given in Table A1 to A3 of theExamples section.

Concerning SGT1 polypeptides, preferred splice variants are splicevariants of a nucleic acid represented by SEQ ID NO: 1, or a splicevariant of a nucleic acid encoding an orthologue or paralogue of SEQ IDNO: 2. Preferably, the amino acid sequence encoded by the splicevariant, when used in the construction of a phylogenetic tree, clusterswith the group of SGT1 polypeptides comprising the amino acid sequencerepresented by SEQ ID NO: 2 rather than with any other group.

Concerning CLC-pKG polypeptides, preferred splice variants are splicevariants of a nucleic acid represented by SEQ ID NO: 53, or a splicevariant of a nucleic acid encoding an orthologue or paralogue of SEQ IDNO: 54. Preferably, the amino acid sequence encoded by the splicevariant, when used in the construction of a phylogenetic tree, such asthe one depicted in FIG. 1 of Marmagne et al. 2007 (herein incorporatedby reference), clusters with the group of CLC polypeptides of bacterialorigin, preferably with SCLC (P74477) from Synechocystis sp.; or withthe group of plant origin comprising AtCLCe and AtCLCf than with anyother anion group.

Concerning HD-hydrolase-like polypeptides, preferred splice variants aresplice variants of a nucleic acid represented by SEQ ID NO: 118, or asplice variant of a nucleic acid encoding an orthologue or paralogue ofSEQ ID NO: 119. Preferably, the amino acid sequence encoded by thesplice variant, when used in the construction of a phylogenetic tree,such as the one depicted in FIG. 10, clusters with the group ofHD-hydrolase-like polypeptides comprising the amino acid sequencerepresented by SEQ ID NO: 119 rather than with any other group and/orcomprises any one or more of the motifs 11 to 26 defined above.

Another nucleic acid variant useful in performing the methods of theinvention is an allelic variant of a nucleic acid encoding an SGT1polypeptide, or a CLC-pKG polypeptide, or a HD-hydrolase-likepolypeptide, as defined hereinabove, an allelic variant being as definedherein.

According to the present invention, there is provided a method forenhancing yield-related traits in plants, comprising introducing andexpressing in a plant an allelic variant of any one of the nucleic acidsgiven in Table A1 to A3 of the Examples section, or comprisingintroducing and expressing in a plant an allelic variant of a nucleicacid encoding an orthologue, paralogue or homologue of any of the aminoacid sequences given in Table A1 to A3 of the Examples section.

Concerning SGT1 polypeptides, the polypeptides encoded by allelicvariants useful in the methods of the present invention havesubstantially the same biological activity as the SGT1 polypeptide ofSEQ ID NO: 2 and any of the amino acids depicted in Table A1 of theExamples section. Allelic variants exist in nature, and encompassedwithin the methods of the present invention is the use of these naturalalleles. Preferably, the allelic variant is an allelic variant of SEQ IDNO: 1 or an allelic variant of a nucleic acid encoding an orthologue orparalogue of SEQ ID NO: 2. Preferably, the amino acid sequence encodedby the allelic variant, when used in the construction of a phylogenetictree, clusters with the SGT1 polypeptides comprising the amino acidsequence represented by SEQ ID NO: 2 rather than with any other group.

Concerning CLC-pKG polypeptides, the polypeptides encoded by allelicvariants useful in the methods of the present invention havesubstantially the same biological activity as the CLC-pKG polypeptide ofSEQ ID NO: 54 and any of the amino acids depicted in Table A2 of theExamples section. Allelic variants exist in nature, and encompassedwithin the methods of the present invention is the use of these naturalalleles. Preferably, the allelic variant is an allelic variant of SEQ IDNO: 53 or an allelic variant of a nucleic acid encoding an orthologue orparalogue of SEQ ID NO: 54. Preferably, the amino acid sequence encodedby the allelic variant, when used in the construction of a phylogenetictree, such as the one depicted in FIG. 1 of Marmagne et al. 2007 (hereinincorporated by reference), clusters with the group of CLC polypeptidesof bacterial origin, preferably with SCLC (P74477) from Synechocystissp.; or with the group of plant origin comprising AtCLCe and AtCLCf thanwith any other anion group.

Concerning HD-hydrolase-like polypeptides, the polypeptides encoded byallelic variants useful in the methods of the present invention havesubstantially the same biological activity as the HD-hydrolase-likepolypeptide of SEQ ID NO: 119 and any of the amino acids depicted inTable A3 of the Examples section. Allelic variants exist in nature, andencompassed within the methods of the present invention is the use ofthese natural alleles. Preferably, the allelic variant is an allelicvariant of SEQ ID NO: 118 or an allelic variant of a nucleic acidencoding an orthologue or paralogue of SEQ ID NO: 119. Preferably, theamino acid sequence encoded by the allelic variant, when used in theconstruction of a phylogenetic tree, such as the one depicted in FIG.10, clusters with the group of HD-hydrolase-like polypeptides comprisingthe amino acid sequence represented by SEQ ID NO: 119 rather than withany other group and/or comprises any one or more of the motifs 11 to 26defined above.

Gene shuffling or directed evolution may also be used to generatevariants of nucleic acids encoding SGT1 polypeptides, or CLC-pKGpolypeptides, or HD-hydrolase-like polypeptides, as defined above; theterm “gene shuffling” being as defined herein.

According to the present invention, there is provided a method forenhancing yield-related traits in plants, comprising introducing andexpressing in a plant a variant of any one of the nucleic acid sequencesgiven in Table A1 to A3 of the Examples section, or comprisingintroducing and expressing in a plant a variant of a nucleic acidencoding an orthologue, paralogue or homologue of any of the amino acidsequences given in Table A1 to A3 of the Examples section, which variantnucleic acid is obtained by gene shuffling.

Concerning SGT1 polypeptides, preferably, the amino acid sequenceencoded by the variant nucleic acid obtained by gene shuffling, whenused in the construction of a phylogenetic tree, clusters with the groupof SGT1 polypeptides comprising the amino acid sequence represented bySEQ ID NO: 2 rather than with any other group.

Concerning CLC-pKG polypeptides, preferably, the amino acid sequenceencoded by the variant nucleic acid obtained by gene shuffling, whenused in the construction of a phylogenetic tree such as the one depictedin FIG. 1 of Marmagne et al. 2007 (herein incorporated by reference),clusters with the group of CLC polypeptides of bacterial origin,preferably with SCLC (P74477) from Synechocystis sp.; or with the groupof plant origin comprising AtCLCe and AtCLCf than with any other aniongroup.

Concerning HD-hydrolase-like polypeptides, preferably, the amino acidsequence encoded by the variant nucleic acid obtained by gene shuffling,when used in the construction of a phylogenetic tree, such as the onedepicted in FIG. 10, clusters with the group of HD-hydrolase-likepolypeptides comprising the amino acid sequence represented by SEQ IDNO: 119 rather than with any other group and/or comprises any one ormore of the motifs 11 to 26 defined above.

Furthermore, nucleic acid variants may also be obtained by site-directedmutagenesis. Several methods are available to achieve site-directedmutagenesis, the most common being PCR based methods (Current Protocolsin Molecular Biology. Wiley Eds.).

Nucleic acids encoding SGT1 polypeptides may be derived from any naturalor artificial source. The nucleic acid may be modified from its nativeform in composition and/or genomic environment through deliberate humanmanipulation. Preferably the SGT1 polypeptide-encoding nucleic acid isfrom a plant, further preferably from pepper, most preferably thenucleic acid is from Capsicum annuum.

Nucleic acids encoding CLC-pKG polypeptides may be derived from anynatural or artificial source. The nucleic acid may be modified from itsnative form in composition and/or genomic environment through deliberatehuman manipulation. Preferably the CLC-pKG polypeptide-encoding nucleicacid is from a cyanobacterial origin, further preferably fromSynechocystis species, most preferably from Synechocystis sp. PCC 6803.

Nucleic acids encoding HD-hydrolase-like polypeptides may be derivedfrom any natural or artificial source. The nucleic acid may be modifiedfrom its native form in composition and/or genomic environment throughdeliberate human manipulation. Preferably the HD-hydrolase-likepolypeptide-encoding nucleic acid is from a plant or a bacterium,further preferably from a cyanophyte, more preferably from the familyChroococcaceae, most preferably the nucleic acid is from Synechocystissp.

Performance of the methods of the invention gives plants having enhancedyield-related traits. In particular, performance of the methods of theinvention gives plants having increased yield, especially increased seedyield relative to control plants. The terms “yield” and “seed yield” aredescribed in more detail in the “definitions” section herein.

Reference herein to enhanced yield-related traits is taken to mean anincrease early vigour and/or in biomass (weight) of one or more parts ofa plant, which may include aboveground (harvestable) parts and/or(harvestable) parts below ground. In particular, such harvestable partsare seeds, and performance of the methods of the invention results inplants having increased seed yield relative to the seed yield of controlplants.

The present invention provides a method for increasing yield-relatedtraits, especially seed yield in plants, relative to control plants,which method comprises modulating expression in a plant of a nucleicacid encoding an SGT1 polypeptide, or a CLC-pKG polypeptide, or aHD-hydrolase-like polypeptide, as defined herein.

Since the transgenic plants according to the present invention haveincreased yield and/or increased yield-related traits, it is likely thatthese plants exhibit an increased growth rate (during at least part oftheir life cycle), relative to the growth rate of control plants at acorresponding stage in their life cycle.

According to a preferred feature of the present invention, performanceof the methods of the invention gives plants having an increased growthrate relative to control plants. Therefore, according to the presentinvention, there is provided a method for increasing the growth rate ofplants, which method comprises modulating expression in a plant of anucleic acid encoding an SGT1 polypeptide, or a CLC-pKG polypeptide, ora HD-hydrolase-like polypeptide, as defined herein.

Performance of the methods of the invention gives plants grown undernon-stress conditions or under mild drought conditions increased yieldrelative to control plants grown under comparable conditions. Therefore,according to the present invention, there is provided a method forincreasing yield in plants grown under non-stress conditions or undermild drought conditions, which method comprises modulating expression ina plant of a nucleic acid encoding an SGT1 polypeptide, or a CLC-pKGpolypeptide, or a HD-hydrolase-like polypeptide.

Performance of the methods of the invention gives plants grown underconditions of nutrient deficiency, particularly under conditions ofnitrogen deficiency, increased yield relative to control plants grownunder comparable conditions. Therefore, according to the presentinvention, there is provided a method for increasing yield in plantsgrown under conditions of nutrient deficiency, which method comprisesmodulating expression in a plant of a nucleic acid encoding an SGT1polypeptide, or a CLC-pKG polypeptide, or a HD-hydrolase-likepolypeptide.

Performance of the methods of the invention gives plants grown underconditions of salt stress, increased yield relative to control plantsgrown under comparable conditions. Therefore, according to the presentinvention, there is provided a method for increasing yield in plantsgrown under conditions of salt stress, which method comprises modulatingexpression in a plant of a nucleic acid encoding an SGT1 polypeptide, ora CLC-pKG polypeptide, or a HD-hydrolase-like polypeptide.

The invention also provides genetic constructs and vectors to facilitateintroduction and/or expression in plants of nucleic acids encoding anSGT1 polypeptide, or a CLC-pKG polypeptide, or a HD-hydrolase-likepolypeptide. The gene constructs may be inserted into vectors, which maybe commercially available, suitable for transforming into plants andsuitable for expression of the gene of interest in the transformedcells. The invention also provides use of a gene construct as definedherein in the methods of the invention.

More specifically, the present invention provides a constructcomprising:

-   -   (a) a nucleic acid encoding an SGT1 polypeptide, or a CLC-pKG        polypeptide, or a HD-hydrolase-like polypeptide, as defined        above;    -   (b) one or more control sequences capable of driving expression        of the nucleic acid sequence of (a); and optionally    -   (c) a transcription termination sequence.

Preferably, the nucleic acid encoding an SGT1 polypeptide, or a CLC-pKGpolypeptide, or a HD-hydrolase-like polypeptide, is as defined above.The term “control sequence” and “termination sequence” are as definedherein.

Plants are transformed with a vector comprising any of the nucleic acidsdescribed above. The skilled artisan is well aware of the geneticelements that must be present on the vector in order to successfullytransform, select and propagate host cells containing the sequence ofinterest. The sequence of interest is operably linked to one or morecontrol sequences (at least to a promoter).

Concerning SGT1 polypeptides, advantageously, any type of promoter,whether natural or synthetic, may be used to drive expression of thenucleic acid sequence, but preferably the promoter is of plant origin. Aroot-specific promoter is particularly useful in the methods. Theroot-specific promoter is preferably an RCc3 promoter (Plant Mol Biol.1995 January; 27(2):237-48), more preferably the RCc3 promoter is fromrice, further preferably the RCc3 promoter is represented by a nucleicacid sequence substantially similar to SEQ ID NO: 50, most preferablythe promoter is as represented by SEQ ID NO: 50. Examples of otherroot-specific promoters which may also be used to perform the methods ofthe invention are shown in Table 2b in the “Definitions” section above.

Concerning CLC-pKG polypeptides, advantageously, any type of promoter,whether natural or synthetic, may be used to drive expression of thenucleic acid sequence, but preferably the promoter is of plant origin. Aroot promoter is particularly useful in the methods. Preferably the rootpromoter is ubiquitous within the root. Also useful in the methods ofthe invention is constitutive promoter. Preferably the constitutivepromoter is a ubiquitous constitutive promoter of medium strength. Seethe “Definitions” section herein for definitions of the various promotertypes.

Concerning HD-hydrolase-like polypeptides, advantageously, any type ofpromoter, whether natural or synthetic, may be used to drive expressionof the nucleic acid sequence, but preferably the promoter is of plantorigin. A constitutive promoter is particularly useful in the methods.Preferably the constitutive promoter is a ubiquitous constitutivepromoter of medium strength. See the “Definitions” section herein fordefinitions of the various promoter types.

Concerning SGT1 polypeptides, it should be clear that the applicabilityof the present invention is not restricted to the SGT1polypeptide-encoding nucleic acid represented by SEQ ID NO: 1, nor isthe applicability of the invention restricted to expression of a SGT1polypeptide-encoding nucleic acid when driven by a root-specificpromoter.

Optionally, one or more terminator sequences may be used in theconstruct introduced into a plant. Preferably, the construct comprisesan expression cassette comprising an RCc3 promoter, substantiallysimilar to SEQ ID NO: 50, and the nucleic acid encoding an SGT1polypeptide.

According to a preferred feature of the invention, the modulatedexpression is increased expression. Methods for increasing expression ofnucleic acids or genes, or gene products, are well documented in the artand examples are provided in the definitions section.

Concerning CLC-pKG polypeptides, it should be clear that theapplicability of the present invention is not restricted to the CLC-pKGpolypeptide-encoding nucleic acid represented by SEQ ID NO: 53, nor isthe applicability of the invention restricted to expression of a CLC-pKGpolypeptide-encoding nucleic acid when driven by root-specific apromoter, or when driven by a constitutive promoter.

The constitutive promoter is preferably a medium strength promoter, morepreferably selected from a plant derived promoter, such as a GOS2promoter, more preferably is the promoter GOS2 promoter from rice.

According to another preferred feature of the invention, the nucleicacid encoding a CLC-pKG polypeptide is operably linked to aroot-specific promoter. The root-specific promoter is preferably an RCc3promoter (Plant Mol Biol. 1995 January; 27(2):237-48), more preferablythe RCc3 promoter is from rice, further preferably the RCc3 promoter isrepresented by a nucleic acid sequence substantially similar to SEQ IDNO: 115, most preferably the promoter is as represented by SEQ ID NO:115. Examples of other root-specific promoters which may also be used toperform the methods of the invention are shown in Table 2b in the“Definitions” section above.

According to a preferred feature of the invention, the modulatedexpression is increased expression. Methods for increasing expression ofnucleic acids or genes, or gene products, are well documented in the artand examples are provided in the definitions section.

Concerning HD-hydrolase-like polypeptides, it should be clear that theapplicability of the present invention is not restricted to theHD-hydrolase-like polypeptide-encoding nucleic acid represented by SEQID NO: 118, nor is the applicability of the invention restricted toexpression of a HD-hydrolase-like polypeptide-encoding nucleic acid whendriven by a constitutive promoter.

The constitutive promoter is preferably a medium strength promoter ofplant origin, such as a GOS2 promoter, more preferably the promoter isthe GOS2 promoter from rice. Further preferably the constitutivepromoter is represented by a nucleic acid sequence substantially similarto SEQ ID NO: 164, most preferably the constitutive promoter is asrepresented by SEQ ID NO: 164. See the “Definitions” section herein forfurther examples of constitutive promoters.

Optionally, one or more terminator sequences may be used in theconstruct introduced into a plant. Preferably, the construct comprisesan expression cassette comprising a GOS2 promoter, substantially similarto SEQ ID NO: 164, and the nucleic acid encoding the HD-hydrolase-likepolypeptide.

According to a preferred feature of the invention, the modulatedexpression is increased expression. Methods for increasing expression ofnucleic acids or genes, or gene products, are well documented in the artand examples are provided in the definitions section.

As mentioned above, a preferred method for modulating expression of anucleic acid encoding an SGT1 polypeptide, or a CLC-pKG polypeptide, ora HD-hydrolase-like polypeptide, is by introducing and expressing in aplant a nucleic acid encoding an SGT1 polypeptide, or a CLC-pKGpolypeptide, or a HD-hydrolase-like polypeptide respectively; howeverthe effects of performing the method, i.e. enhancing yield-relatedtraits may also be achieved using other well known techniques, includingbut not limited to T-DNA activation tagging, TILLING, homologousrecombination. A description of these techniques is provided in thedefinitions section.

The invention also provides a method for the production of transgenicplants having enhanced yield-related traits relative to control plants,comprising introduction and expression in a plant of any nucleic acidencoding an SGT1 polypeptide, or a CLC-pKG polypeptide, or aHD-hydrolase-like polypeptide, as defined hereinabove.

More specifically, the present invention provides a method for theproduction of transgenic plants having enhanced yield-related traits,particularly increased (seed) yield, which method comprises:

-   -   (i) introducing and expressing in a plant or plant cell nucleic        acid encoding an SGT1 polypeptide, or a CLC-pKG polypeptide, or        a HD-hydrolase-like polypeptide; and    -   (ii) cultivating the plant cell under conditions promoting plant        growth and development.

The nucleic acid of (i) may be any of the nucleic acids capable ofencoding an SGT1 polypeptide, or a CLC-pKG polypeptide, or aHD-hydrolase-like polypeptide, as defined herein.

The nucleic acid may be introduced directly into a plant cell or intothe plant itself (including introduction into a tissue, organ or anyother part of a plant). According to a preferred feature of the presentinvention, the nucleic acid is preferably introduced into a plant bytransformation. The term “transformation” is described in more detail inthe “definitions” section herein.

The present invention clearly extends to any plant cell or plantproduced by any of the methods described herein, and to all plant partsand propagules thereof. The present invention encompasses plants orparts thereof (including seeds) obtainable by the methods according tothe present invention. The plants or parts thereof comprise a nucleicacid transgene encoding an SGT1 polypeptide, or a CLC-pKG polypeptide,or a HD-hydrolase-like polypeptide, as defined above. The presentinvention extends further to encompass the progeny of a primarytransformed or transfected cell, tissue, organ or whole plant that hasbeen produced by any of the aforementioned methods, the only requirementbeing that progeny exhibit the same genotypic and/or phenotypiccharacteristic(s) as those produced by the parent in the methodsaccording to the invention.

The invention also includes host cells containing an isolated nucleicacid encoding an SGT1 polypeptide, or a CLC-pKG polypeptide, or aHD-hydrolase-like polypeptide, as defined hereinabove. Preferred hostcells according to the invention are plant cells. Host plants for thenucleic acids or the vector used in the method according to theinvention, the expression cassette or construct or vector are, inprinciple, advantageously all plants, which are capable of synthesizingthe polypeptides used in the inventive method.

The methods of the invention are advantageously applicable to any plant.Plants that are particularly useful in the methods of the inventioninclude all plants which belong to the superfamily Viridiplantae, inparticular monocotyledonous and dicotyledonous plants including fodderor forage legumes, ornamental plants, food crops, trees or shrubs.According to a preferred embodiment of the present invention, the plantis a crop plant. Examples of crop plants include soybean, sunflower,canola, alfalfa, rapeseed, linseed, cotton, tomato, potato and tobacco.Further preferably, the plant is a monocotyledonous plant. Examples ofmonocotyledonous plants include sugarcane. More preferably the plant isa cereal. Examples of cereals include rice, maize, wheat, barley,millet, rye, triticale, sorghum, emmer, spelt, secale, einkorn, teff,milo and oats.

The invention also extends to harvestable parts of a plant such as, butnot limited to seeds, leaves, fruits, flowers, stems, roots, rhizomes,tubers and bulbs, which harvestable parts comprise a recombinant nucleicacid encoding an SGT1 polypeptide, or a CLC-pKG polypeptide, or aHD-hydrolase-like polypeptide. The invention furthermore relates toproducts derived, preferably directly derived, from a harvestable partof such a plant, such as dry pellets or powders, oil, fat and fattyacids, starch or proteins.

The present invention also encompasses use of nucleic acids encodingSGT1 polypeptides, or CLC-pKG polypeptides, or HD-hydrolase-likepolypeptides, as described herein and use of these SGT1 polypeptides, orCLC-pKG polypeptides, or HD-hydrolase-like polypeptides, in enhancingany of the aforementioned yield-related traits in plants. For example,nucleic acids encoding an SGT1 polypeptide, or a CLC-pKG polypeptide, ora HD-hydrolase-like polypeptide, described herein, or the SGT1polypeptides, or CLC-pKG polypeptides, or HD-hydrolase-likepolypeptides, themselves, may find use in breeding programmes in which aDNA marker is identified which may be genetically linked to geneencoding an SGT1 polypeptide, or a CLC-pKG polypeptide, or aHD-hydrolase-like polypeptide. The nucleic acids/genes, or the SGT1polypeptides, or CLC-pKG polypeptides, or HD-hydrolase-likepolypeptides, may be used to define a molecular marker. This DNA orprotein marker may then be used in breeding programmes to select plantshaving enhanced yield-related traits as defined hereinabove in themethods of the invention. Furthermore, allelic variants of nucleicacid/gene encoding an SGT1 polypeptide, or a CLC-pKG polypeptide, or aHD-hydrolase-like polypeptide, may find use in marker-assisted breedingprogrammes. Nucleic acids encoding an SGT1 polypeptide, or a CLC-pKGpolypeptide, or a HD-hydrolase-like polypeptide, may also be used asprobes for genetically and physically mapping the genes that they are apart of, and as markers for traits linked to those genes. Suchinformation may be useful in plant breeding in order to develop lineswith desired phenotypes.

Items

1. SGT1 Polypeptides

In one aspect, the invention is characterised by any of the followingitems

-   -   1. A method for enhancing yield-related traits in plants        relative to control plants, comprising modulating expression in        a plant of a nucleic acid encoding an SGT1 polypeptide, wherein        said SGT1 polypeptide comprises the following in any order:        -   (i) at least one tetratricopeptide (TPR) repeat;        -   (ii) at least one CS domain; and        -   (iii) an SGS domain.    -   2. Method according to item 1, wherein said modulated expression        is effected by introducing and expressing in a plant a nucleic        acid encoding an SGT1 polypeptide.    -   3. Method according to item 1 or 2, wherein said nucleic acid        encoding an SGT1 polypeptide encodes any one of the proteins        listed in Table A1 or is a portion of such a nucleic acid, or a        nucleic acid capable of hybridising with such a nucleic acid.    -   4. Method according to any one of items 1 to 3, wherein said        nucleic acid sequence encodes an orthologue or paralogue of any        of the proteins given in Table A1.    -   5. Method according to any preceding item, wherein said enhanced        yield-related traits comprise increased seed yield relative to        control plants.    -   6. Method according to any one of items 1 to 5, wherein said        enhanced yield-related traits are obtained under non-stress        conditions.    -   7. Method according to any one of items 2 to 6, wherein said        nucleic acid is operably linked to a root-specific promoter,        preferably to an RCc3 promoter, most preferably to an RCc3        promoter from rice.    -   8. Method according to any one of items 1 to 7, wherein said        nucleic acid encoding a SGT1 polypeptide is of plant origin,        preferably from Capsicum annuum a dicotyledonous plant, further        preferably from the family Solanaceae, more preferably from the        genus Capsicum, most preferably from Capsicum annuum.    -   9. Plant or part thereof, including seeds, obtainable by a        method according to any one of items 1 to 8, wherein said plant        or part thereof comprises a recombinant nucleic acid encoding an        SGT1 polypeptide.    -   10. Construct comprising:        -   (i) nucleic acid encoding an SGT1 polypeptide as defined in            item 1;        -   (ii) one or more control sequences capable of driving            expression of the nucleic acid sequence of (a); and            optionally        -   (iii) a transcription termination sequence.    -   11. Construct according to item 10, wherein one of said control        sequences is a root-specific promoter, preferably an RCc3        promoter, most preferably an RCc3 promoter from rice.    -   12. Use of a construct according to item 10 or 11 in a method        for making plants having increased yield, particularly increased        seed yield relative to control plants.    -   13. Plant, plant part or plant cell transformed with a construct        according to item 10 or 11.    -   14. Method for the production of a transgenic plant having        increased yield, particularly increased seed yield relative to        control plants, comprising:        -   (i) introducing and expressing in a plant a nucleic acid            encoding an SGT1 polypeptide as defined in item 1; and        -   (ii) cultivating the plant cell under conditions promoting            plant growth and development.    -   15. Transgenic plant having increased yield, particularly        increased seed yield, relative to control plants, resulting from        modulated expression of a nucleic acid encoding an SGT1        polypeptide as defined in item 1, or a transgenic plant cell        derived from said transgenic plant.    -   16. Transgenic plant according to item 9, 13 or 15, or a        transgenic plant cell derived thereof, wherein said plant is a        crop plant or a monocot or a cereal, such as rice, maize, wheat,        barley, millet, rye, triticale, sorghum emmer, spelt, secale,        einkorn, teff, milo and oats.    -   17. Harvestable parts of a plant according to item 16, wherein        said harvestable parts are preferably shoot biomass and/or        seeds.    -   18. Products derived from a plant according to item 16 and/or        from harvestable parts of a plant according to item 17.    -   19. Use of a nucleic acid encoding an SGT1 polypeptide in        increasing yield, particularly in increasing seed yield relative        to control plants.    -   20. Use of a nucleic acid encoding an SGT1 polypeptide as a        molecular marker for plants having increased yield, particularly        increased seed yield.

2. CLC-pKG Polypeptides

In another aspect, the invention is characterised by any of thefollowing items

-   -   1. A method for enhancing yield-related traits in plants        relative to control plants, comprising modulating expression in        a plant of a nucleic acid encoding a CLC-pKG polypeptide,        wherein said CLC-pKG polypeptide comprises a Voltage_CLC domain        (Pfam entry PF00654) and a CBS domain (Pfam entry PF00571) and        optionally a USP domain (PF00582).    -   2. Method according to item 1, wherein said CLC-pKG polypeptide        comprises a domain having in increasing order of preference at        least 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%,        36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%,        49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%,        62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%,        75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%,        88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or        100% sequence identity to:        -   (i) a CLC in SEQ ID NO: 54 as represented by the sequence            located between amino acids 77 and 422 of SEQ ID NO: 54;        -   (ii) a CBS domain in SEQ ID NO: 54 as represented by the            sequence located between amino acids 455 to 510 or 516 to            571 SEQ ID NO: 54; and optionally        -   (iii) a USP domain in SEQ ID NO: 54 as represented by the            sequence located between amino acids 597-731 of SEQ ID NO:            54.    -   3. Method according to item 1 or 2, wherein said modulated        expression is effected by introducing and expressing in a plant        a genetic construct comprising a nucleic acid encoding a CLC-pKG        polypeptide.    -   4. Method according to any one of items 1 to 3, wherein said        nucleic acid encoding a CLC-pKG polypeptide encodes any one of        the proteins listed in Table A2 or is a portion of such a        nucleic acid, or a nucleic acid capable of hybridising with such        a nucleic acid.    -   5. Method according to any one of items 1 to 4, wherein said        nucleic acid encodes an orthologue or paralogue of any of the        proteins given in Table A2.    -   6. Method according to any preceding item, wherein said enhanced        yield-related traits comprise increased yield, preferably        increased biomass and/or increased seed yield relative to        control plants.    -   7. Method according to any one of items 1 to 6, wherein said        enhanced yield-related traits are obtained under non-stress        conditions or under conditions of drought stress, or salt        stress.    -   8. Method according to any one of items 3 to 7, wherein said        nucleic acid is operably linked to a constitutive promoter,        preferably to a RCc3 promoter, most preferably to a RCc3        promoter from rice.    -   9. Method according to any one of items 1 to 8, wherein said        nucleic acid encoding a CLC-pKG polypeptide is of cyanobacterial        origin, further preferably from Synechosystis species, more        preferably from Synechocystis sp. PCC 6803.    -   10. Plant or part thereof, including seeds, obtainable by a        method according to any one of items 1 to 9, wherein said plant        or part thereof comprises a recombinant nucleic acid encoding a        CLC-pKG polypeptide.    -   11. Construct comprising:        -   (i) nucleic acid encoding a CLC-pKG polypeptide as defined            in items 1 or 2;        -   (ii) one or more control sequences capable of driving            expression of the nucleic acid sequence of (a); and            optionally        -   (iii) a transcription termination sequence.    -   12. Construct according to item 11, wherein one of said control        sequences is a constitutive promoter, preferably a RCc3        promoter, most preferably a RCc3 promoter from rice.    -   13. Use of a construct according to item 11 or 12 in a method        for making plants having increased yield, particularly increased        biomass and/or increased seed yield relative to control plants.    -   14. Plant, plant part or plant cell transformed with a construct        according to item 11 or 12.    -   15. Method for the production of a transgenic plant having        increased yield, particularly increased biomass and/or increased        seed yield relative to control plants, comprising:        -   (i) introducing and expressing in a plant a nucleic acid            encoding a CLC-pKG polypeptide as defined in item 1 or 2;            and        -   (ii) cultivating the plant cell under conditions promoting            plant growth and development.    -   16. Transgenic plant having increased yield, particularly        increased biomass and/or increased seed yield, relative to        control plants, resulting from modulated expression of a        recombinant nucleic acid encoding a CLC-pKG polypeptide as        defined in item 1 or 2, or a transgenic plant cell derived from        said transgenic plant.    -   17. Transgenic plant according to item 10, 14 or 16, or a        transgenic plant cell derived thereof, wherein said plant is a        crop plant or a monocot or a cereal, such as rice, maize, wheat,        barley, millet, rye, triticale, sorghum emmer, spelt, secale,        einkorn, teff, milo and oats.    -   18. Harvestable parts of a plant according to item 17, wherein        said harvestable parts are preferably shoot biomass and/or        seeds.    -   19. Products derived from a plant according to item 17 and/or        from harvestable parts of a plant according to item 18.    -   20. Use of a genetic construct comprising a nucleic acid        encoding a CLC-pKG polypeptide in increasing yield, particularly        in increasing seed yield and/or shoot biomass in plants,        relative to control plants.

3. HD-Hydrolase-Like Polypeptides

In yet another aspect, the invention is characterised by any of thefollowing items

-   -   1. A method for enhancing yield-related traits in plants        relative to control plants, comprising modulating expression in        a plant of a nucleic acid encoding a HD-hydrolase-like        polypeptide, wherein said HD-hydrolase-like polypeptide        comprises a CRISPR-associated protein Crm2 domain.    -   2. Method according to item 1, wherein said HD-hydrolase-like        polypeptide comprises one or more of the motifs 11 to 26.    -   3. Method according to item 1 or 2, wherein said modulated        expression is effected by introducing and expressing in a plant        a nucleic acid encoding a HD-hydrolase-like polypeptide.    -   4. Method according to any one of items 1 to 3, wherein said        nucleic acid encoding a HD-hydrolase-like polypeptide encodes        any one of the proteins listed in Table A3 or is a portion of        such a nucleic acid, or a nucleic acid capable of hybridising        with such a nucleic acid.    -   5. Method according to any one of items 1 to 4, wherein said        nucleic acid sequence encodes an orthologue or paralogue of any        of the proteins given in Table A3.    -   6. Method according to any preceding item, wherein said enhanced        yield-related traits comprise increased yield, preferably        increased biomass and/or increased seed yield relative to        control plants.    -   7. Method according to any one of items 1 to 6, wherein said        enhanced yield-related traits are obtained under non-stress        conditions.    -   8. Method according to any one of items 3 to 7, wherein said        nucleic acid is operably linked to a constitutive promoter,        preferably to a GOS2 promoter, most preferably to a GOS2        promoter from rice.    -   9. Method according to any one of items 1 to 8, wherein said        nucleic acid encoding a HD-hydrolase-like polypeptide is of        plant origin, preferably from a cyanophyte, further preferably        from the family Chroococcaceae, more preferably from the genus        Synechocystis.    -   10. Plant or part thereof, including seeds, obtainable by a        method according to any one of items 1 to 9, wherein said plant        or part thereof comprises a recombinant nucleic acid encoding a        HD-hydrolase-like polypeptide.    -   11. Construct comprising:        -   (i) nucleic acid encoding a HD-hydrolase-like polypeptide as            defined in items 1 or 2;        -   (ii) one or more control sequences capable of driving            expression of the nucleic acid sequence of (a); and            optionally        -   (iii) a transcription termination sequence.    -   12. Construct according to item 11, wherein one of said control        sequences is a constitutive promoter, preferably a GOS2        promoter, most preferably a GOS2 promoter from rice.    -   13. Use of a construct according to item 11 or 12 in a method        for making plants having increased yield, particularly increased        biomass and/or increased seed yield relative to control plants.    -   14. Plant, plant part or plant cell transformed with a construct        according to item 11 or 12.    -   15. Method for the production of a transgenic plant having        increased yield, particularly increased biomass and/or increased        seed yield relative to control plants, comprising:        -   (i) introducing and expressing in a plant a nucleic acid            encoding a HD-hydrolase-like polypeptide as defined in item            1 or 2; and        -   (ii) cultivating the plant cell under conditions promoting            plant growth and development.    -   16. Transgenic plant having increased yield, particularly        increased biomass and/or increased seed yield, relative to        control plants, resulting from modulated expression of a nucleic        acid encoding a HD-hydrolase-like polypeptide as defined in item        1 or 2, or a transgenic plant cell derived from said transgenic        plant.    -   17. Transgenic plant according to item 10, 14 or 16, or a        transgenic plant cell derived thereof, wherein said plant is a        crop plant or a monocot or a cereal, such as rice, maize, wheat,        barley, millet, rye, triticale, sorghum emmer, spelt, secale,        einkorn, teff, milo and oats.    -   18. Harvestable parts of a plant according to item 17, wherein        said harvestable parts are preferably shoot biomass and/or        seeds.    -   19. Products derived from a plant according to item 17 and/or        from harvestable parts of a plant according to item 18.    -   20. Use of a nucleic acid encoding a HD-hydrolase-like        polypeptide in increasing yield, particularly in increasing seed        yield and/or shoot biomass in plants, relative to control        plants.

DESCRIPTION OF FIGURES

The present invention will now be described with reference to thefollowing figures in which:

FIG. 1 represents a multiple alignment of various SGT1 polypeptides.Alignment of polypeptide sequences was performed using the ClustalW 2.0algorithm of progressive alignment (Thompson et al. (1997) Nucleic AcidsRes 25:4876-4882; Chenna et al. (2003). Nucleic Acids Res 31:3497-3500)with standard setting (slow alignment, similarity matrix: Gonnet, gapopening penalty 10, gap extension penalty: 0.2). Minor manual editingwas done to further optimise the alignment. The SGT1 polypeptides arealigned in FIG. 2. A. thaliana_AT4G23570.1#1: SEQ ID NO: 4; A.thaliana_AT4G23570.2#1: SEQ ID NO: 6; A. thaliana_AT4G23570.3#1: SEQ IDNO: 10; A. thaliana_AT4G11260.1#1: SEQ ID NO: 8; B.napus_BN06MC26625_(—)51284379@2: SEQ ID NO: 12; Z.mays_ZM07MC27211_BFb0187N13@: SEQ ID NO: 34; Z.mays_ZM07MC23831_BFb0038K08@: SEQ ID NO: 36; O.sativa_LOC_Os01g43540.1#1: SEQ ID NO: 20; T. aestivum_TC280790#1: SEQ IDNO: 32; M. truncatula_CT025844_(—)7.4#1: SEQ ID NO: 18; G.max_GM06MC38560_sab91h08@375: SEQ ID NO: 14;TraitMillCDS_(—)25598_CDS6534_(—)69_: SEQ ID NO: 2;SGT1_from_Pepper_KOGENT2_: SEQ ID NO: 2; S. lycopersicum_TC192025#1: SEQID NO: 26; S. lycopersicum_NP9243669#1: SEQ ID NO: 28; P.trichocarpa_scaff_IV.839#1: SEQ ID NO: 22; P.trichocarpa_scaff_(—)44.273#1: SEQ ID NO: 24; S.lycopersicum_AW398985#1: SEQ ID NO: 30; and H.vulgare_c62589592hv270303@64: SEQ ID NO: 16.

FIG. 2 shows a further alignment highlighting the conserved domainscommon to SGT1 polypeptides. CaSGT1: SEQ ID NO: 167; NbSGT1: SEQ ID NO:168; HvSGT1: SEQ ID NO: 169; OsSGT1: SEQ ID NO: 170; BoSGT1: SEQ ID NO:171; AtSGT1b: SEQ ID NO: 172; and AtSGT1a: SEQ ID NO: 173.

FIG. 3 shows a phylogenetic tree of SGT1 polypeptides constructed usinga neighbour-joining clustering algorithm as provided in the AlignXprogramme from the Vector NTI (Invitrogen).

FIG. 4 represents the binary vector used for increased expression inOryza sativa of an SGT1-encoding nucleic acid under the control of arice RCc3 promoter (pRCc3).

FIG. 5 represents a multiple alignment of various CLC-pKG polypeptides.The asterisks indicate identical amino acids among the various proteinsequences, colons represent highly conserved amino acid substitutions,and the dots represent less conserved amino acid substitution; on otherpositions there is no sequence conservation. These alignments can beused for defining further motifs, when using conserved amino acids.gi|218440518|ref|YP_(—)002378847.: SEQ ID NO: 56;gi|196258397|ref|ZP_(—)03156931.1: SEQ ID NO: 58;gi|126659209|ref|ZP_(—)01730347.1: SEQ ID NO: 60;gi|172034995|ref|YP_(—)001801496.: SEQ ID NO: 62;gi|67923321|ref|ZP_(—)00516804.11: SEQ ID NO: 66;gi|218248189|ref|YP_(—)002373560.: SEQ ID NO: 64;gi|159026894|emb|CAO89145.1|_e: SEQ ID NO: 68;gi|166366612|ref|YP_(—)001658885.: SEQ ID NO: 70;gi|16331172|ref|NP_(—)441900.1|_c: SEQ ID NO: 54;gi|170077188|ref|YP_(—)001733826.: SEQ ID NO: 72;gi|158334130|ref|YP_(—)001515302.: SEQ ID NO: 108;gi|119510301|ref|ZP_(—)01629437.1: SEQ ID NO: 74;gi|186682049|ref|YP_(—)001865245.: SEQ ID NO: 96;gi|75908381|ref|YP_(—)322677.1|_C: SEQ ID NO: 90;gi|17232383|ref|NP_(—)488931.1|_h: SEQ ID NO: 92;gi|225516217|ref|ZP_(—)03763190.1: SEQ ID NO: 98;gi|254413597|ref|ZP_(—)05027367.1: SEQ ID NO: 76;gi|186683293|ref|YP_(—)001866489.: SEQ ID NO: 78;gi|225522175|ref|ZP_(—)03768989.1: SEQ ID NO: 86;gi|186682226|ref|YP_(—)001865422.: SEQ ID NO: 88;gi|220909579|ref|YP_(—)002484890.: SEQ ID NO: 102;gi|37523751|ref|NP_(—)927128.1|_c: SEQ ID NO: 104;gi|119486852|ref|ZP_(—)01620827.1: SEQ ID NO: 100;gi|209525724|ref|ZP_(—)03274261.1: SEQ ID NO: 106;gi|220908306|ref|YP_(—)002483617.: SEQ ID NO: 110; andgi|81300397|ref|YP_(—)400605.1|_C: SEQ ID NO: 112.

FIG. 6 shows phylogenetic tree of CLC-pKG polypeptides.

FIG. 7 represents the binary vector used for increased expression inOryza sativa of a CLC-PKG-encoding nucleic acid under the control of arice RCc3 promoter (pRCc3).

FIG. 8 represents the domain structure of SEQ ID NO: 119 with conservedmotifs 11 to 26, underlined and numbered. The CRISPR-associated proteinCrm2 (IPR013407) domain is shown in bold.

FIG. 9 represents a multiple alignment of various HD-hydrolase-likepolypeptides. The asterisks indicate identical amino acids among thevarious protein sequences, colons represent highly conserved amino acidsubstitutions, and the dots represent less conserved amino acidsubstitution; on other positions there is no sequence conservation.These alignments can be used for defining further motifs, when usingconserved amino acids. gi|121997427|ref|YP_(—)001002214.: SEQ ID NO:133; gi|88810314|ref|ZP_(—)01125571.1|: SEQ ID NO: 147;gi|255254649|ref|ZP_(—)05334193.1: SEQ ID NO: 135;gi|255338062|ref|ZP_(—)05378933.1: SEQ ID NO: 137;gi|20808984|ref|NP_(—)624155.1|_h: SEQ ID NO: 139;gi|254478158|ref|ZP_(—)05091540.1: SEQ ID NO: 141;gi|38505758|ref|NP_(—)942378.1|_h: SEQ ID NO: 119;gi|170079601|ref|YP_(—)001736234.: SEQ ID NO: 121;gi|126661502|ref|ZP_(—)01732553.1: SEQ ID NO: 125;gi|172035267|ref|YP_(—)001801768.: SEQ ID NO: 127;gi|86608324|ref|YP_(—)477086.1|_C: SEQ ID NO: 123;gi|86607166|ref|YP_(—)475929.1|_C: SEQ ID NO: 129;gi|255256456|ref|ZP_(—)05335917.1: SEQ ID NO: 145;gi|209526382|ref|ZP_(—)03274910.1: SEQ ID NO: 131; andgi|162453956|ref|YP_(—)001616323.: SEQ ID NO: 143.

FIG. 10 shows phylogenetic tree of HD-hydrolase-like polypeptides. Theidentifiers are the accession numbers as provided for the proteins inthe sequence listing.

FIG. 11 represents the binary vector used for increased expression inOryza sativa of a HD-hydrolase-like-encoding nucleic acid under thecontrol of a rice GOS2 promoter (pGOS2).

EXAMPLES

The present invention will now be described with reference to thefollowing examples, which are by way of illustration alone. Thefollowing examples are not intended to completely define or otherwiselimit the scope of the invention.

DNA manipulation: unless otherwise stated, recombinant DNA techniquesare performed according to standard protocols described in (Sambrook(2001) Molecular Cloning: a laboratory manual, 3rd Edition Cold SpringHarbor Laboratory Press, CSH, N.Y.) or in Volumes 1 and 2 of Ausubel etal. (1994), Current Protocols in Molecular Biology, Current Protocols.Standard materials and methods for plant molecular work are described inPlant Molecular Biology Labfax (1993) by R. D. D. Croy, published byBIOS Scientific Publications Ltd (UK) and Blackwell ScientificPublications (UK).

Example 1 Identification of Sequences Related to the Nucleic AcidSequence Used in the Methods of the Invention

1. SGT1 Polypeptides

Sequences (full length cDNA, ESTs or genomic) related to SEQ ID NO: 1and SEQ ID NO: 2 were identified amongst those maintained in the EntrezNucleotides database at the National Center for BiotechnologyInformation (NCBI) using database sequence search tools, such as theBasic Local Alignment Tool (BLAST) (Altschul et al. (1990) J. Mol. Biol.215:403-410; and Altschul et al. (1997) Nucleic Acids Res.25:3389-3402). The program is used to find regions of local similaritybetween sequences by comparing nucleic acid or polypeptide sequences tosequence databases and by calculating the statistical significance ofmatches. For example, the polypeptide encoded by the nucleic acid of SEQID NO: 1 was used for the TBLASTN algorithm, with default settings andthe filter to ignore low complexity sequences set off. The output of theanalysis was viewed by pairwise comparison, and ranked according to theprobability score (E-value), where the score reflect the probabilitythat a particular alignment occurs by chance (the lower the E-value, themore significant the hit). In addition to E-values, comparisons werealso scored by percentage identity. Percentage identity refers to thenumber of identical nucleotides (or amino acids) between the twocompared nucleic acid (or polypeptide) sequences over a particularlength. In some instances, the default parameters may be adjusted tomodify the stringency of the search. For example the E-value may beincreased to show less stringent matches. This way, short nearly exactmatches may be identified.

Table A1 provides a list of nucleic acid sequences related to SEQ ID NO:1 and SEQ ID NO: 2.

TABLE A1 Examples of SGT1 nucleic acids and polypeptides: Nucleic acidPolypeptide Name SEQ ID NO: SEQ ID NO: SGT1 from Pepper 1 2A.thaliana_AT4G23570.1#1 3 4 A.thaliana_AT4G23570.2#1 5 6A.thaliana_AT4G11260.1#1 7 8 A.thaliana_AT4G23570.3#1 9 10B.napus_BN06MC26625_51284379@26524#1 11 12G.max_GM06MC38560_sab91h08@37598#1 13 14H.vulgare_c62589592hv270303@6491#1 15 16 M.truncatula_CT025844_7.4#1 1718 O.sativa_LOC_Os01g43540.1#1 19 20 P.trichocarpa_scaff_IV.839#1 21 22P.trichocarpa_scaff_44.273#1 23 24 S.lycopersicum_TC192025#1 25 26S.lycopersicum_NP9243669#1 27 28 S.lycopersicum_AW398985#1 29 30T.aestivum_TC280790#1 31 32 Z.mays_ZM07MC27211_BFb0187N13@27130#1 33 34Z.mays_ZM07MC23831_BFb0038K08@23765#1 35 36

Sequences have been tentatively assembled and publicly disclosed byresearch institutions, such as The Institute for Genomic Research (TIGR;beginning with TA). The Eukaryotic Gene Orthologs (EGO) database may beused to identify such related sequences, either by keyword search or byusing the BLAST algorithm with the nucleic acid sequence or polypeptidesequence of interest. Special nucleic acid sequence databases have beencreated for particular organisms, such as by the Joint Genome Institute.

2. CLC-pKG Polypeptides

Sequences (full length cDNA, ESTs or genomic) related to SEQ ID NO: 53and SEQ ID NO: 54 were identified amongst those maintained in the EntrezNucleotides database at the National Center for BiotechnologyInformation (NCBI) using database sequence search tools, such as theBasic Local Alignment Tool (BLAST) (Altschul et al. (1990) J. Mol. Biol.215:403-410; and Altschul et al. (1997) Nucleic Acids Res.25:3389-3402). The program is used to find regions of local similaritybetween sequences by comparing nucleic acid or polypeptide sequences tosequence databases and by calculating the statistical significance ofmatches. For example, the polypeptide encoded by the nucleic acid of SEQID NO: 53 was used for the TBLASTN algorithm, with default settings andthe filter to ignore low complexity sequences set off. The output of theanalysis was viewed by pairwise comparison, and ranked according to theprobability score (E-value), where the score reflect the probabilitythat a particular alignment occurs by chance (the lower the E-value, themore significant the hit). In addition to E-values, comparisons werealso scored by percentage identity. Percentage identity refers to thenumber of identical nucleotides (or amino acids) between the twocompared nucleic acid (or polypeptide) sequences over a particularlength. In some instances, the default parameters may be adjusted tomodify the stringency of the search. For example the E-value may beincreased to show less stringent matches. This way, short nearly exactmatches may be identified.

Table A2 provides a list of nucleic acid sequences and polypeptidesrelated to SEQ ID NO: 53 and SEQ ID NO: 54.

TABLE A2 Examples of CLC-pKG polypeptides: Nucleic acid Organism Nucleicacid name SEQ ID NO Synechocystis sp. PCC 6803]gi|16329170:2216476-2219175 53 Cyanothece sp. PCC 7424]gi|218437013:4004295-4006922 55 Cyanothece sp. PCC 7822]gi|196258358:38011-40635 57 Cyanothece sp. CCY0110]gi|126659182:36041-38674 59 Cyanothece sp. ATCC 51142]gi|172034917:71619-74267 61 Cyanothece sp. PCC 8801]gi|218244892:3580780-3583419 63 Crocosphaera watsonii WH 8501]gi|67923302:15782-18430 65 Microcystis aeruginosa PCC 7806]gi|159026870:19707-22334 67 Microcystis aeruginosa NIES-843]gi|166362741:3545508-3548135 69 Synechococcus sp. PCC 7002]gi|170076636:589624-592260 71 Nodularia spumigena CCY9414]gi|119510275:28473-31136 73 Microcoleus chthonoplastes PCC 7420]gi|254413420:221158-223773 75 Nostoc punctiforme PCC 73102]gi|186680550:3804594-3807185 77 Nostoc punctiforme PCC 73102]gi|186680550:2232857-2235448 79 Anabaena variabilis ATCC 29413]gi|75906225:2674416-2677004 81 Nostoc sp. PCC 7120]gi|17227497:5827615-5830230 83 ‘Nostoc azollae’ 0708]gi|225522173:3082-5673 85 Nostoc punctiforme PCC 73102]gi|186680550:2232857-2235448 87 Anabaena variabilis ATCC 29413]gi|75906225:2674416-2677004 89 Nostoc sp. PCC 7120]gi|17227497:5827615-5830230 91 ‘Nostoc azollae’ 0708]gi|225522173:3082-5673 93 Nostoc punctiforme PCC 73102]gi|186680550:1989068-1991719 95 ‘Nostoc azollae’ 0708]gi|225516157:49369-51948 97 Lyngbya sp. PCC 8106]gi|119486739:136813-139515 99 Cyanothece sp. PCC 7425]gi|220905643:4270175-4272766 101 Gloeobacter violaceus PCC 7421]gi|37519569:4380220-4382796 103 Arthrospira maxima CS-328]gi|209525652:71572-74244 105 Acaryochloris marina MBIC11017]gi|158333233:913406-916021 107 Cyanothece sp. PCC 7425]gi|220905643:2873784-2876477 109 Synechococcus elongatus PCC 7942]gi|81298811:1653255-1655834 111 Polypeptide Organism Polypeptide nameSEQ ID NO Synechocystis sp. PCC 6803] gi|16331172|ref|NP_441900 54Cyanothece sp. PCC 7424] gi|218440518|ref|YP_002378847 56 Cyanothece sp.PCC 7822] gi|196258397|ref|ZP_03156931 58 Cyanothece sp. CCY0110]gi|126659209|ref|ZP_01730347 60 Cyanothece sp. ATCC 51142]gi|172034995|ref|YP_001801496 62 Cyanothece sp. PCC 8801]gi|218248189|ref|YP_002373560 64 Crocosphaera watsonii WH 8501]gi|67923321|ref|ZP_00516804 66 Microcystis aeruginosa PCC 7806]gi|159026894|emb|CAO89145 68 Microcystis aeruginosa NIES-843]gi|166366612|ref|YP_001658885 70 Synechococcus sp. PCC 7002]gi|170077188|ref|YP_001733826 72 Nodularia spumigena CCY9414]gi|119510301|ref|ZP_01629437 74 Microcoleus chthonoplastes PCC 7420]gi|254413597|ref|ZP_05027367 76 Nostoc punctiforme PCC 73102]gi|186683293|ref|YP_001866489 78 Nostoc punctiforme PCC 73102]gi|186682226|ref|YP_001865422 80 Anabaena variabilis ATCC 29413]gi|75908381|ref|YP_322677 82 Nostoc sp. PCC 7120]gi|17232383|ref|NP_488931 84 ‘Nostoc azollae’ 0708]gi|225522175|ref|ZP_03768989 86 Nostoc punctiforme PCC 73102]gi|186682226|ref|YP_001865422 88 Anabaena variabilis ATCC 29413]gi|75908381|ref|YP_322677 90 Nostoc sp. PCC 7120]gi|17232383|ref|NP_488931 92 ‘Nostoc azollae’ 0708]gi|225522175|ref|ZP_03768989 94 Nostoc punctiforme PCC 73102]gi|186682049|ref|YP_001865245 96 ‘Nostoc azollae’ 0708]gi|225516217|ref|ZP_03763190 98 Lyngbya sp. PCC 8106]gi|119486852|ref|ZP_01620827 100 Cyanothece sp. PCC 7425]gi|220909579|ref|YP_002484890 102 Gloeobacter violaceus PCC 7421]gi|37523751|ref|NP_927128 104 Arthrospira maxima CS-328]gi|209525724|ref|ZP_03274261 106 Acaryochloris marina MBIC11017]gi|158334130|ref|YP_001515302 108 Cyanothece sp. PCC 7425]gi|220908306|ref|YP_002483617 110 Synechococcus elongatus PCC 7942]gi|81300397|ref|YP_400605 112

Sequences have been tentatively assembled and publicly disclosed byresearch institutions, such as The Institute for Genomic Research (TIGR;beginning with TA). The Eukaryotic Gene Orthologs (EGO) database may beused to identify such related sequences, either by keyword search or byusing the BLAST algorithm with the nucleic acid sequence or polypeptidesequence of interest. Special nucleic acid sequence databases have beencreated for particular organisms, such as by the Joint Genome Institute.Furthermore, access to proprietary databases, has allowed theidentification of novel nucleic acid and polypeptide sequences.

3. HD-Hydrolase-Like Polypeptides

Sequences (full length cDNA, ESTs or genomic) related to SEQ ID NO: 118and SEQ ID NO: 119 were identified amongst those maintained in theEntrez Nucleotides database at the National Center for BiotechnologyInformation (NCBI) using database sequence search tools, such as theBasic Local Alignment Tool (BLAST) (Altschul et al. (1990) J. Mol. Biol.215:403-410; and Altschul et al. (1997) Nucleic Acids Res.25:3389-3402). The program is used to find regions of local similaritybetween sequences by comparing nucleic acid or polypeptide sequences tosequence databases and by calculating the statistical significance ofmatches. For example, the polypeptide encoded by the nucleic acid of SEQID NO: 118 was used for the TBLASTN algorithm, with default settings andthe filter to ignore low complexity sequences set off. The output of theanalysis was viewed by pairwise comparison, and ranked according to theprobability score (E-value), where the score reflect the probabilitythat a particular alignment occurs by chance (the lower the E-value, themore significant the hit). In addition to E-values, comparisons werealso scored by percentage identity. Percentage identity refers to thenumber of identical nucleotides (or amino acids) between the twocompared nucleic acid (or polypeptide) sequences over a particularlength. In some instances, the default parameters may be adjusted tomodify the stringency of the search. For example the E- value may beincreased to show less stringent matches. This way, short nearly exactmatches may be identified.

Table A3 provides a list of nucleic acid sequences related to SEQ ID NO:118 and SEQ ID NO: 119.

TABLE A3 Examples of HD-hydrolase-like nucleic acids and polypeptides:Nucleic acid Polypeptide Name Source SEQ ID NO: SEQ ID NO: NP_942378.1Synechocystis sp. 118 119 YP_001736234.1 Synechococcus sp. 120 121YP_477086.1 Synechococcus sp. 122 123 ZP_01732553.1 Cyanothece sp. 124125 YP_001801768.1 Cyanothece sp. 126 127 YP_475929.1 Synechococcus sp.128 129 ZP_03274910.1 Arthrospira maxima 130 131 YP_001002214.1Halorhodospira 132 133 halophila ZP_05334193.1 Thermoanaerobacter 134135 italicus ZP_05378933.1 Thermoanaerobacter 136 137 mathranii subsp.Mathranii NP_624155.1 Thermoanaerobacter 138 139 tengcongensisZP_05091540.1 Carboxydibrachium 140 141 pacificum YP_001616323.1Sorangium cellulosum 142 143 ZP_05335917.1 Thermoanaerobacterium 144 145thermosaccharolyticum ZP_01125571.1 Nitrococcus mobilis 146 147

Sequences have been tentatively assembled and publicly disclosed byresearch institutions, such as The Institute for Genomic Research (TIGR;beginning with TA). The Eukaryotic Gene Orthologs (EGO) database may beused to identify such related sequences, either by keyword search or byusing the BLAST algorithm with the nucleic acid sequence or polypeptidesequence of interest. Special nucleic acid sequence databases have beencreated for particular organisms, such as by the Joint Genome Institute.Furthermore, access to proprietary databases, has allowed theidentification of novel nucleic acid and polypeptide sequences.

Example 2 Alignment of Sequences Related to the Polypeptide SequencesUsed in the Methods of the Invention

1. SGT1 Polypeptides

Alignment of polypeptide sequences was performed using the ClustalW 2.0algorithm of progressive alignment (Thompson et al. (1997) Nucleic AcidsRes 25:4876-4882; Chenna et al. (2003). Nucleic Acids Res 31:3497-3500)with standard setting (slow alignment, similarity matrix: Gonnet, gapopening penalty 10, gap extension penalty: 0.2). Minor manual editingwas done to further optimise the alignment. The SGT1 polypeptides arealigned in FIGS. 1 and 2.

A phylogenetic tree of SGT1 polypeptides (FIG. 3) was constructed usinga neighbour-joining clustering algorithm as provided in the AlignXprogramme from the Vector NTI (Invitrogen).

2. CLC-pKG Polypeptides

Alignment of polypeptide sequences was performed using the ClustalW 1.8algorithm of progressive alignment (Thompson et al. (1997) Nucleic AcidsRes 25:4876-4882; Chenna et al. (2003). Nucleic Acids Res 31:3497-3500)with standard setting (slow alignment, similarity matrix: Blosum 62, gapopening penalty 10, gap extension penalty: 0.2). Minor manual editingwas done to further optimise the alignment. The CLC-pKG polypeptides arealigned in FIG. 5.

A phylogenetic tree of CLC-pKG polypeptides (FIG. 6) was taken fromMarmagne et al. 2007.

3. HD-Hydrolase-Like Polypeptides

Alignment of polypeptide sequences was performed using the ClustalW 1.81algorithm of progressive alignment (Thompson et al. (1997) Nucleic AcidsRes 25:4876-4882; Chenna et al. (2003). Nucleic Acids Res 31:3497-3500)with standard setting (slow alignment, similarity matrix: Gonnet, gapopening penalty 10, gap extension penalty: 0.2). Minor manual editingwas done to further optimise the alignment.

A phylogenetic tree of HD-hydrolase-like polypeptides (FIG. 10) wasconstructed using a neighbour-joining clustering algorithm as providedin the AlignX program of Vector NTI (Invitrogen).

Example 3 Calculation of Global Percentage Identity Between PolypeptideSequences Useful in Performing the Methods of the Invention

1. SGT1 Polypeptides

Global percentages of similarity and identity between full lengthpolypeptide sequences useful in performing the methods of the inventionwere determined using one of the methods available in the art, theMatGAT (Matrix Global Alignment Tool) software (BMC Bioinformatics. 20034:29. MatGAT: an application that generates similarity/identity matricesusing protein or DNA sequences. Campanella J J, Bitincka L, Smalley J;software hosted by Ledion Bitincka). MatGAT software generatessimilarity/identity matrices for DNA or protein sequences withoutneeding pre-alignment of the data. The program performs a series ofpair-wise alignments using the Myers and Miller global alignmentalgorithm (with a gap opening penalty of 12, and a gap extension penaltyof 2), calculates similarity and identity using for example Blosum 62(for polypeptides), and then places the results in a distance matrix.

Parameters used in the comparison are: Scoring matrix: Blosum62, FirstGap: 12, Extending Gap: 2.

A MATGAT table for local alignment of a specific domain, or data on %identity/similarity between specific domains may also be performed.

2. CLC-pKG Polypeptides

Global percentages of similarity and identity between full lengthpolypeptide sequences useful in performing the methods of the inventionwere determined using one of the methods available in the art, theMatGAT (Matrix Global Alignment Tool) software (BMC Bioinformatics. 20034:29. MatGAT: an application that generates similarity/identity matricesusing protein or DNA sequences. Campanella J J, Bitincka L, Smalley J;software hosted by Ledion Bitincka). MatGAT software generatessimilarity/identity matrices for DNA or protein sequences withoutneeding pre-alignment of the data. The program performs a series ofpair-wise alignments using the Myers and Miller global alignmentalgorithm (with a gap opening penalty of 12, and a gap extension penaltyof 2), calculates similarity and identity using for example Blosum 62(for polypeptides), and then places the results in a distance matrix.Parameters typically used in the comparisons are: Scoring matrix:Blosum62, First Gap: 12, Extending Gap: 2.

3. HD-Hydrolase-Like Polypeptides

Global percentages of similarity and identity between full lengthpolypeptide sequences useful in performing the methods of the inventionwere determined using one of the methods available in the art, theMatGAT (Matrix Global Alignment Tool) software (BMC Bioinformatics. 20034:29. MatGAT: an application that generates similarity/identity matricesusing protein or DNA sequences. Campanella J J, Bitincka L, Smalley J;software hosted by Ledion Bitincka). MatGAT software generatessimilarity/identity matrices for DNA or protein sequences withoutneeding pre-alignment of the data. The program performs a series ofpair-wise alignments using the Myers and Miller global alignmentalgorithm (with a gap opening penalty of 12, and a gap extension penaltyof 2), calculates similarity and identity using for example Blosum 62(for polypeptides), and then places the results in a distance matrix.Sequence similarity is shown in the bottom half of the dividing line andsequence identity is shown in the top half of the diagonal dividingline.

Parameters used in the comparison were: Scoring matrix: Blosum62, FirstGap: 12, Extending Gap: 2.

Results of the software analysis are shown in Table B1 for the globalsimilarity and identity over the full length of the polypeptidesequences. The sequence identity (in %) between the HD-hydrolase-likepolypeptide sequences useful in performing the methods of the inventioncan be as low as 17% compared to SEQ ID NO: 118 (NP_(—)942378.1).

TABLE B1 MatGAT results for global similarity and identity over the fulllength of the polypeptide sequences. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 1. NP_942378.1 68.1 48.3 51.5 47.2 48.3 27.2 19.6 23.6 23.5 21.5 21.517.2 20.5 20.4  2. YP_001736234.1 80.1 46.4 50.7 46.7 49.3 27.9 19.725.5 24.5 21.0 20.9 19.9 22.6 22.8  3. ZP_01732553.1 61.8 61.0 44.7 45.544.0 25.7 15.4 19.4 18.9 21.2 21.3 22.2 19.0 18.9  4. YP_477086.1 66.766.2 59.3 78.1 47.5 28.2 21.2 26.0 24.0 21.2 21.2 18.1 21.5 21.0  5.YP_475929.1 62.6 60.9 61.2 83.8 44.2 27.9 20.8 24.3 23.6 20.1 20.0 17.520.6 20.3  6. YP_001801768.1 63.5 64.4 58.2 65.1 59.6 26.7 19.5 23.422.4 22.9 21.9 18.7 20.9 20.4  7. ZP_03274910.1 44.6 46.3 40.4 47.1 44.847.9 18.7 21.8 19.9 19.3 19.4 17.7 20.5 20.1  8. YP_001616323.1 33.734.1 28.4 34.3 32.7 35.1 33.9 24.1 23.4 18.3 18.3 15.4 20.1 20.2  9.YP_001002214.1 42.2 41.8 36.0 41.7 39.4 40.3 37.5 34.6 56.1 25.4 25.520.2 26.3 26.6 10. ZP_01125571.1 38.8 40.5 35.4 40.8 40.3 39.1 36.2 35.966.8 24.9 24.8 19.6 26.7 27.2 11. ZP_05334193.1 39.4 39.8 39.8 41.2 40.441.4 35.6 34.3 42.9 45.5 99.4 29.2 26.3 26.7 12. ZP_05378933.1 39.1 39.740.4 40.9 40.5 41.8 35.6 34.2 43.0 45.6 99.8 29.3 26.4 26.7 13.ZP_05335917.1 33.8 36.4 38.7 35.5 35.3 35.2 32.5 28.8 35.1 37.6 47.847.8 22.3 22.6 14. NP_624155.1 40.2 40.3 37.2 41.1 41.4 39.4 37.8 33.543.3 44.6 48.4 48.4 40.6 97.6 15. ZP_05091540.1 40.2 40.8 36.9 40.1 41.139.3 37.6 33.5 43.5 44.4 49.1 49.4 40.4 98.6

Example 4 Identification of Domains Comprised in Polypeptide SequencesUseful in Performing the Methods of the Invention

1. SGT1 Polypeptides

The Integrated Resource of Protein Families, Domains and Sites(InterPro) database is an integrated interface for the commonly usedsignature databases for text- and sequence-based searches. The InterProdatabase combines these databases, which use different methodologies andvarying degrees of biological information about well-characterizedproteins to derive protein signatures. Collaborating databases includeSWISS-PROT, PROSITE, TrEMBL, PRINTS, ProDom and Pfam, Smart andTIGRFAMs. Pfam is a large collection of multiple sequence alignments andhidden Markov models covering many common protein domains and families.Pfam is hosted at the Sanger Institute server in the United Kingdom.Interpro is hosted at the European Bioinformatics Institute in theUnited Kingdom.

The results of the InterPro scan of the polypeptide sequence asrepresented by SEQ ID NO: 2 are presented in Table C1.

Sequence Search Results

Show the detailed description of the results page

We found 6 Pfam-A matches to your search sequence (3 significant and 3insignificant).

You did not choose to search for Pfam-B matches on your sequence:

Show the search options and sequence that you submitted.

Return to the search form to look for Pfam domains on a new sequence.

Significant Pfam-A Matches

Show or hide all alignments

TABLE C1 InterPro scan results (major accession numbers)of the polypeptide sequence as represented by SEQ ID NO: 2. EntrySequence HMM Alignment Pfam-A Description type Start End From ToBit score E-value method TPR_1 Tetratricopeptide Repeat  70 103 1 34 21.0 7.3e-05 fs repeat #HMM *->aeayynlGnaylklgkydeAieayekALeldPnn<-*#MATCH    ++ay ++G+a++kl++y+ A +a+e   +l P #SEQSKAYLRKGLACMKLEEYQTAKQQLETGASLAPGE      103 CS CS domain Domain 172 2481 83  94.3 7.3e-05 fs #HMM *->prydWyQtldeVtitiplkgvfpikkkdvkVeilprslkvsikqpgggkpylldgepLfgp #MATCH r+++yQ ++eV++ti++kg+   ++k+v+V+++++ l+vsi +pgg + y ++   Lfg+ #SEQYRHEFYQKPEEVVVTIFAKGI---PAKNVVVDFGEQILSVSIDLPGG-ETYSFQPR-LFGK #HMMIdpeeSswkiedtkkveItLkK<-* #MATCH I p ++ + +++t k+eI L K #SEQITPAKCRYEVMST-KIEIRLAK   248 SGS SGS domain Domain 287 368 1 91 168.19.9e-53 ls #HMM *->kKnWDkLtaveKrlkevkKEekisedEkldGeAALnnlFKklYeDgDddmkRAMmKSftES #MATCH     +WDkL+a      +vkKEek   dEkldG+AALn++F+++Y+D+D+d++RAMmKSf+ES #SEQ   NVDWDKLEA------QVKKEEK---DEKLDGDAALNKFFRDIYKDADEDTRRAMMKSFVES #HMM   nGTvLSTNWkdVgkkkVetkPpeGmEpKew<-* #MATCH   nGTvLSTNWk Vg kkVe++Pp+GmE+K+w #SEQ    NGTVLSTNWKKVGTKKVEGSPPDGMELKKW

2. CLC-pKG Polypeptides

The Integrated Resource of Protein Families, Domains and Sites(InterPro) database is an integrated interface for the commonly usedsignature databases for text- and sequence-based searches. The InterProdatabase combines these databases, which use different methodologies andvarying degrees of biological information about well-characterizedproteins to derive protein signatures. Collaborating databases includeSWISS-PROT, PROSITE, TrEMBL, PRINTS, ProDom and Pfam, Smart andTIGRFAMs. Pfam is a large collection of multiple sequence alignments andhidden Markov models covering many common protein domains and families.Pfam is hosted at the Sanger Institute server in the United Kingdom.Interpro is hosted at the European Bioinformatics Institute in theUnited Kingdom.

The results of the pfam scan of the polypeptide sequence as representedby SEQ ID NO: 54 are presented in Table C2.

TABLE C2 pfam scan results (major accession numbers) of the polypeptidesequence as represented by SEQ ID NO: 54. Amino acid Accessioncoordinates on Database number Accession name SEQ ID NO 54 Pfam PF00571Voltage Gate Chloride  77-422 Channel Pfam PF00571 CBS domain 455-510Pfam PF00571 CBS domain 516-571 Pfam PF00582 Universal Stress Protein597-731 Family

3. HD-Hydrolase-Like Polypeptides

The Integrated Resource of Protein Families, Domains and Sites(InterPro) database is an integrated interface for the commonly usedsignature databases for text- and sequence-based searches. The InterProdatabase combines these databases, which use different methodologies andvarying degrees of biological information about well-characterizedproteins to derive protein signatures. Collaborating databases includeSWISS-PROT, PROSITE, TrEMBL, PRINTS, ProDom and Pfam, Smart andTIGRFAMs. Pfam is a large collection of multiple sequence alignments andhidden Markov models covering many common protein domains and families.Pfam is hosted at the Sanger Institute server in the United Kingdom.Interpro is hosted at the European Bioinformatics Institute in theUnited Kingdom.

The results of the InterPro scan of the polypeptide sequence asrepresented by SEQ ID NO: 119 are presented in Table C3.

TABLE C3 InterPro scan results (major accession numbers) of thepolypeptide sequence as represented by SEQ ID NO: 119. Amino acidAccession coordinates on Database number Accession name SEQ ID NO 119InterPro IPR013407 CRISPR-associated protein Crm2 HMMTigr TIGR02577cas_TM1794_Crm2: [221-842] CRISPR-associated pr 8.7e−13

Example 5 Topology Prediction of the Polypeptide Sequences Useful inPerforming the Methods of the Invention

1. SGT1 Polypeptides

TargetP 1.1 predicts the subcellular location of eukaryotic proteins.The location assignment is based on the predicted presence of any of theN-terminal pre-sequences: chloroplast transit peptide (cTP),mitochondrial targeting peptide (mTP) or secretory pathway signalpeptide (SP). Scores on which the final prediction is based are notreally probabilities, and they do not necessarily add to one. However,the location with the highest score is the most likely according toTargetP, and the relationship between the scores (the reliability class)may be an indication of how certain the prediction is. The reliabilityclass (RC) ranges from 1 to 5, where 1 indicates the strongestprediction. TargetP is maintained at the server of the TechnicalUniversity of Denmark.

For the sequences predicted to contain an N-terminal pre-sequence apotential cleavage site can also be predicted.

A number of parameters are selected, such as organism group (non-plantor plant), cutoff sets (none, predefined set of cutoffs, oruser-specified set of cutoffs), and the calculation of prediction ofcleavage sites (yes or no).

Many other algorithms can be used to perform such analyses, including:

-   -   ChloroP 1.1 hosted on the server of the Technical University of        Denmark;    -   Protein Prowler Subcellular Localisation Predictor version 1.2        hosted on the server of the Institute for Molecular Bioscience,        University of Queensland, Brisbane, Australia;    -   PENCE Proteome Analyst PA-GOSUB 2.5 hosted on the server of the        University of Alberta, Edmonton, Alberta, Canada;    -   TMHMM, hosted on the server of the Technical University of        Denmark    -   PSORT (URL: psort.org)    -   PLOC (Park and Kanehisa, Bioinformatics, 19, 1656-1663, 2003).

2. CLC-pKG Polypeptides

TargetP 1.1 predicts the subcellular location of eukaryotic proteins.The location assignment is based on the predicted presence of any of theN-terminal pre-sequences: chloroplast transit peptide (cTP),mitochondrial targeting peptide (mTP) or secretory pathway signalpeptide (SP). Scores on which the final prediction is based are notreally probabilities, and they do not necessarily add to one. However,the location with the highest score is the most likely according toTargetP, and the relationship between the scores (the reliability class)may be an indication of how certain the prediction is. The reliabilityclass (RC) ranges from 1 to 5, where 1 indicates the strongestprediction. TargetP is maintained at the server of the TechnicalUniversity of Denmark.

For the sequences predicted to contain an N-terminal presequence apotential cleavage site can also be predicted.

In addition or alternatively, many other algorithms can be used toperform such analyses, including:

-   -   ChloroP 1.1 hosted on the server of the Technical University of        Denmark;    -   Protein Prowler Subcellular Localisation Predictor version 1.2        hosted on the server of the Institute for Molecular Bioscience,        University of Queensland, Brisbane, Australia;    -   PENCE Proteome Analyst PA-GOSUB 2.5 hosted on the server of the        University of Alberta, Edmonton, Alberta, Canada;    -   TMHMM, hosted on the server of the Technical University of        Denmark    -   PSORT (URL: psort.org)    -   PLOC (Park and Kanehisa, Bioinformatics, 19, 1656-1663, 2003).

3. HD-Hydrolase-Like Polypeptides

TargetP 1.1 predicts the subcellular location of eukaryotic proteins.The location assignment is based on the predicted presence of any of theN-terminal pre-sequences: chloroplast transit peptide (cTP),mitochondrial targeting peptide (mTP) or secretory pathway signalpeptide (SP). Scores on which the final prediction is based are notreally probabilities, and they do not necessarily add to one. However,the location with the highest score is the most likely according toTargetP, and the relationship between the scores (the reliability class)may be an indication of how certain the prediction is. The reliabilityclass (RC) ranges from 1 to 5, where 1 indicates the strongestprediction. TargetP is maintained at the server of the TechnicalUniversity of Denmark.

For the sequences predicted to contain an N-terminal presequence apotential cleavage site can also be predicted.

A number of parameters were selected, such as organism group (non-plantor plant), cutoff sets (none, predefined set of cutoffs, oruser-specified set of cutoffs), and the calculation of prediction ofcleavage sites (yes or no).

The results of TargetP 1.1 analysis of the polypeptide sequence asrepresented by SEQ ID NO: 119 are presented Table D1. The “plant”organism group has been selected, no cutoffs defined, and the predictedlength of the transit peptide requested. The subcellular localization ofthe polypeptide sequence as represented by SEQ ID NO: 119 may be thecytoplasm or nucleus, no transit peptide is predicted.

TABLE D1 TargetP 1.1 analysis of the polypeptide sequence as representedby SEQ ID NO: 119. Name Len cTP mTP SP other Loc RC TPlen SEQ ID 9790.103 0.321 0.050 0.554 — 4 — NO: 119 cutoff 0.000 0.000 0.000 0.000Abbreviations: Len, Length; cTP, Chloroplastic transit peptide; mTP,Mitochondrial transit peptide, SP, Secretory pathway signal peptide,other, Other subcellular targeting, Loc, Predicted Location; RC,Reliability class; TPlen, Predicted transit peptide length.

Many other algorithms can be used to perform such analyses, including:

-   -   ChloroP 1.1 hosted on the server of the Technical University of        Denmark;    -   Protein Prowler Subcellular Localisation Predictor version 1.2        hosted on the server of the Institute for Molecular Bioscience,        University of Queensland, Brisbane, Australia;    -   PENCE Proteome Analyst PA-GOSUB 2.5 hosted on the server of the        University of Alberta, Edmonton, Alberta, Canada;    -   TMHMM, hosted on the server of the Technical University of        Denmark    -   PSORT (URL: psort.org)    -   PLOC (Park and Kanehisa, Bioinformatics, 19, 1656-1663, 2003).

Example 6 Assay Related to the Polypeptide Sequences Useful inPerforming the Methods of the Invention

1. CLC-pKG Polypeptides

Marmagne et al 2007 described a method functionally complements thegef-1 yeast mutant. In brief, suspensions of the indicated strains W303(WT), RGY86 (gef-1 mutant,) and each transformant (gef-1:CLC-ofinterest) are set up at DO1 (53108 cells). Serial dilutions (d1-d16) arespotted onto the appropriate media. For the low-iron phenotype, a4-folddilution of each suspension may be spotted onto YPEG mediasupplemented with 0.6 mM ferrozine, pH 5.8 (A, B) and grown for 3 d at30_C. For the pH-dependent phenotype, an 8-fold dilution is spotted ontoYPD (C), SD 6 0.1 mM CuSO4, pH 7 (D, E) and SGE 6 CuSO4 0.1 mM, pH7 (F,G) media and is grown for 3 d at 30_C.

In addition or alternatively the patch clamp based method described byDe Angeli (Nature 442, 939-942, 2006) may be used to measure currentsacross the tonoplast. The patch clamp technique is well known in the artfor studying ion channel activity in cells, see for example Hamill etal., Pflugers Archiv (European Journal of Physiology) 391, 85-100, 1981.

Example 7 Cloning of the Nucleic Acid Sequence Used in the Methods ofthe Invention

1. SGT1 Polypeptides

The nucleic acid sequence was amplified by PCR using as template aCapsicum annuum cDNA library (in pCMV Sport 6.0; Invitrogen, Paisley,UK). PCR was performed using Hifi Taq DNA polymerase in standardconditions, using 200 ng of template in a 50 μl PCR mix. The primersused were prm14133 (SEQ ID NO: 51; sense, start codon in bold): 5′-aaaaagcaggctcacaatggagaatgggaaaagagac-3′ and prm14134 (SEQ ID NO: 52;reverse, complementary): 5′-agaaagctgggttggttttaactagttccaccg-3′, whichinclude the AttB sites for Gateway recombination. The amplified PCRfragment was purified also using standard methods. The first step of theGateway procedure, the BP reaction, was then performed, during which thePCR fragment recombined in vivo with the pDONR201 plasmid to produce,according to the Gateway terminology, an “entry clone”, pSGT1. PlasmidpDONR201 was purchased from Invitrogen, as part of the Gateway®technology.

The entry clone comprising SEQ ID NO: 1 was then used in an LR reactionwith a destination vector used for Oryza sativa transformation. Thisvector contained as functional elements within the T-DNA borders: aplant selectable marker; a screenable marker expression cassette; and aGateway cassette intended for LR in vivo recombination with the nucleicacid sequence of interest already cloned in the entry clone. A rice RCc3promoter (SEQ ID NO: 50) for root-specific expression was locatedupstream of this Gateway cassette.

After the LR recombination step, the resulting expression vectorpRCc3::SGT1 (FIG. 4) was transformed into Agrobacterium strain LBA4044according to methods well known in the art.

2. CLC-pKG Polypeptides

The nucleic acid sequence was amplified by PCR using as template acustom-made Synechosystis DNA. PCR was performed using Hifi Taq DNApolymerase in standard conditions, using 200 ng of template in a 50 μlPCR mix. The primers used were:5′-ggggacaagtttgtacaaaaaagcaggcttaaacaatggcttggtttccctttt-3′ (SEQ ID NO:116) and 5′-ggggaccactttgtacaagaaagctgggtttactcgtctagaccgaaatctg-3′ (SEQID NO: 117), which include the AttB sites for Gateway recombination. Theamplified PCR fragment was purified also using standard methods. Thefirst step of the Gateway procedure, the BP reaction, was thenperformed, during which the PCR fragment recombined in vivo with thepDONR201 plasmid to produce, according to the Gateway terminology, an“entry clone”, pCLC-pKG. Plasmid pDONR201 was purchased from Invitrogen,as part of the Gateway® technology.

The entry clone comprising the longest Open Reading Frame of SEQ ID NO:53 was then used in an LR reaction with a destination vector used forOryza sativa transformation. This vector contained as functionalelements within the T-DNA borders: a plant selectable marker; ascreenable marker expression cassette; and a Gateway cassette intendedfor LR in vivo recombination with the nucleic acid sequence of interestalready cloned in the entry clone. A rice RCc3 promoter (SEQ ID NO: 115)for root specific expression was located upstream of this Gatewaycassette.

After the LR recombination step, the resulting expression vectorpGOS2::CLC-pKG (FIG. 7) was transformed into Agrobacterium strainLBA4044 according to methods well known in the art.

3. HD-Hydrolase-Like Polypeptides

The nucleic acid sequence was amplified by PCR using as template acustom-made Synechocystis cDNA library (in pCMV Sport 6.0; Invitrogen,Paisley, UK). PCR was performed using Hifi Taq DNA polymerase instandard conditions, using 200 ng of template in a 50 μl PCR mix. Theprimers used were prm14240 (SEQ ID NO: 165; sense, start codon in bold):5′-ggggacaagtttgtacaaaaaagcaggcttaaa caatgtctgaagtttactggcaag-3′ andprm14239 (SEQ ID NO: 166; reverse, complementary):5′-ggggaccactttgtacaagaaagctgggtttaattgggaa atttaatgtaacg-3′, whichinclude the AttB sites for Gateway recombination. The amplified PCRfragment was purified also using standard methods. The first step of theGateway procedure, the BP reaction, was then performed, during which thePCR fragment recombined in vivo with the pDONR201 plasmid to produce,according to the Gateway terminology, an “entry clone”,pHD-hydrolase-like. Plasmid pDONR201 was purchased from Invitrogen, aspart of the Gateway® technology.

The entry clone comprising SEQ ID NO: 118 was then used in an LRreaction with a destination vector used for Oryza sativa transformation.This vector contained as functional elements within the T-DNA borders: aplant selectable marker; a screenable marker expression cassette; and aGateway cassette intended for LR in vivo recombination with the nucleicacid sequence of interest already cloned in the entry clone. A rice GOS2promoter (SEQ ID NO: 164) for constitutive specific expression waslocated upstream of this Gateway cassette.

After the LR recombination step, the resulting expression vectorpGOS2::HD-hydrolase-like (FIG. 11) was transformed into Agrobacteriumstrain LBA4044 according to methods well known in the art.

Example 8 Plant Transformation

Rice Transformation

The Agrobacterium containing the expression vector was used to transformOryza sativa plants. Mature dry seeds of the rice japonica cultivarNipponbare were dehusked. Sterilization was carried out by incubatingfor one minute in 70% ethanol, followed by 30 minutes in 0.2% HgCl₂,followed by a 6 times 15 minutes wash with sterile distilled water. Thesterile seeds were then germinated on a medium containing 2,4-D (callusinduction medium). After incubation in the dark for four weeks,embryogenic, scutellum-derived calli were excised and propagated on thesame medium. After two weeks, the calli were multiplied or propagated bysubculture on the same medium for another 2 weeks. Embryogenic calluspieces were sub-cultured on fresh medium 3 days before co-cultivation(to boost cell division activity).

Agrobacterium strain LBA4404 containing the expression vector was usedfor co-cultivation. Agrobacterium was inoculated on AB medium with theappropriate antibiotics and cultured for 3 days at 28° C. The bacteriawere then collected and suspended in liquid co-cultivation medium to adensity (OD₆₀₀) of about 1. The suspension was then transferred to aPetri dish and the calli immersed in the suspension for 15 minutes. Thecallus tissues were then blotted dry on a filter paper and transferredto solidified, co-cultivation medium and incubated for 3 days in thedark at 25° C. Co-cultivated calli were grown on 2,4-D-containing mediumfor 4 weeks in the dark at 28° C. in the presence of a selection agent.During this period, rapidly growing resistant callus islands developed.After transfer of this material to a regeneration medium and incubationin the light, the embryogenic potential was released and shootsdeveloped in the next four to five weeks. Shoots were excised from thecalli and incubated for 2 to 3 weeks on an auxin-containing medium fromwhich they were transferred to soil. Hardened shoots were grown underhigh humidity and short days in a greenhouse.

Approximately 35 independent T0 rice transformants were generated forone construct. The primary transformants were transferred from a tissueculture chamber to a greenhouse. After a quantitative PCR analysis toverify copy number of the T-DNA insert, only single copy transgenicplants that exhibit tolerance to the selection agent were kept forharvest of T1 seed. Seeds were then harvested three to five months aftertransplanting. The method yielded single locus transformants at a rateof over 50% (Aldemita and Hodges 1996, Chan et al. 1993, Hiei et al.1994).

Example 9 Transformation of Other Crops

Corn Transformation

Transformation of maize (Zea mays) is performed with a modification ofthe method described by Ishida et al. (1996) Nature Biotech 14(6):745-50. Transformation is genotype-dependent in corn and only specificgenotypes are amenable to transformation and regeneration. The inbredline A188 (University of Minnesota) or hybrids with A188 as a parent aregood sources of donor material for transformation, but other genotypescan be used successfully as well. Ears are harvested from corn plantapproximately 11 days after pollination (DAP) when the length of theimmature embryo is about 1 to 1.2 mm. Immature embryos are cocultivatedwith Agrobacterium tumefaciens containing the expression vector, andtransgenic plants are recovered through organogenesis. Excised embryosare grown on callus induction medium, then maize regeneration medium,containing the selection agent (for example imidazolinone but variousselection markers can be used). The Petri plates are incubated in thelight at 25° C. for 2-3 weeks, or until shoots develop. The green shootsare transferred from each embryo to maize rooting medium and incubatedat 25° C. for 2-3 weeks, until roots develop. The rooted shoots aretransplanted to soil in the greenhouse. T1 seeds are produced fromplants that exhibit tolerance to the selection agent and that contain asingle copy of the T-DNA insert.

Wheat Transformation

Transformation of wheat is performed with the method described by Ishidaet al. (1996) Nature Biotech 14(6): 745-50. The cultivar Bobwhite(available from CIMMYT, Mexico) is commonly used in transformation.Immature embryos are co-cultivated with Agrobacterium tumefacienscontaining the expression vector, and transgenic plants are recoveredthrough organogenesis. After incubation with Agrobacterium, the embryosare grown in vitro on callus induction medium, then regeneration medium,containing the selection agent (for example imidazolinone but variousselection markers can be used). The Petri plates are incubated in thelight at 25° C. for 2-3 weeks, or until shoots develop. The green shootsare transferred from each embryo to rooting medium and incubated at 25°C. for 2-3 weeks, until roots develop. The rooted shoots aretransplanted to soil in the greenhouse. T1 seeds are produced fromplants that exhibit tolerance to the selection agent and that contain asingle copy of the T-DNA insert.

Soybean Transformation

Soybean is transformed according to a modification of the methoddescribed in the Texas A&M U.S. Pat. No. 5,164,310. Several commercialsoybean varieties are amenable to transformation by this method. Thecultivar Jack (available from the Illinois Seed foundation) is commonlyused for transformation. Soybean seeds are sterilised for in vitrosowing. The hypocotyl, the radicle and one cotyledon are excised fromseven-day old young seedlings. The epicotyl and the remaining cotyledonare further grown to develop axillary nodes. These axillary nodes areexcised and incubated with Agrobacterium tumefaciens containing theexpression vector. After the cocultivation treatment, the explants arewashed and transferred to selection media. Regenerated shoots areexcised and placed on a shoot elongation medium. Shoots no longer than 1cm are placed on rooting medium until roots develop. The rooted shootsare transplanted to soil in the greenhouse. T1 seeds are produced fromplants that exhibit tolerance to the selection agent and that contain asingle copy of the T-DNA insert.

Rapeseed/Canola Transformation

Cotyledonary petioles and hypocotyls of 5-6 day old young seedling areused as explants for tissue culture and transformed according to Babicet al. (1998, Plant Cell Rep 17: 183-188). The commercial cultivarWestar (Agriculture Canada) is the standard variety used fortransformation, but other varieties can also be used. Canola seeds aresurface-sterilized for in vitro sowing. The cotyledon petiole explantswith the cotyledon attached are excised from the in vitro seedlings, andinoculated with Agrobacterium (containing the expression vector) bydipping the cut end of the petiole explant into the bacterialsuspension. The explants are then cultured for 2 days on MSBAP-3 mediumcontaining 3 mg/l BAP, 3% sucrose, 0.7% Phytagar at 23° C., 16 hr light.After two days of co-cultivation with Agrobacterium, the petioleexplants are transferred to MSBAP-3 medium containing 3 mg/l BAP,cefotaxime, carbenicillin, or timentin (300 mg/l) for 7 days, and thencultured on MSBAP-3 medium with cefotaxime, carbenicillin, or timentinand selection agent until shoot regeneration. When the shoots are 5-10mm in length, they are cut and transferred to shoot elongation medium(MSBAP-0.5, containing 0.5 mg/l BAP). Shoots of about 2 cm in length aretransferred to the rooting medium (MS0) for root induction. The rootedshoots are transplanted to soil in the greenhouse. T1 seeds are producedfrom plants that exhibit tolerance to the selection agent and thatcontain a single copy of the T-DNA insert.

Alfalfa Transformation

A regenerating clone of alfalfa (Medicago sativa) is transformed usingthe method of (McKersie et al., 1999 Plant Physiol 119: 839-847).Regeneration and transformation of alfalfa is genotype dependent andtherefore a regenerating plant is required. Methods to obtainregenerating plants have been described. For example, these can beselected from the cultivar Rangelander (Agriculture Canada) or any othercommercial alfalfa variety as described by Brown D C W and A Atanassov(1985. Plant Cell Tissue Organ Culture 4: 111-112). Alternatively, theRA3 variety (University of Wisconsin) has been selected for use intissue culture (Walker et al., 1978 Am J Bot 65:654-659). Petioleexplants are cocultivated with an overnight culture of Agrobacteriumtumefaciens C58C1 pMP90 (McKersie et al., 1999 Plant Physiol 119:839-847) or LBA4404 containing the expression vector. The explants arecocultivated for 3 d in the dark on SH induction medium containing 288mg/L Pro, 53 mg/L thioproline, 4.35 g/L K2SO4, and 100 μmacetosyringinone. The explants are washed in half-strengthMurashige-Skoog medium (Murashige and Skoog, 1962) and plated on thesame SH induction medium without acetosyringinone but with a suitableselection agent and suitable antibiotic to inhibit Agrobacterium growth.After several weeks, somatic embryos are transferred to BOi2Ydevelopment medium containing no growth regulators, no antibiotics, and50 g/L sucrose. Somatic embryos are subsequently germinated onhalf-strength Murashige-Skoog medium. Rooted seedlings were transplantedinto pots and grown in a greenhouse. T1 seeds are produced from plantsthat exhibit tolerance to the selection agent and that contain a singlecopy of the T-DNA insert.

Cotton Transformation

Cotton is transformed using Agrobacterium tumefaciens according to themethod described in U.S. Pat. No. 5,159,135. Cotton seeds are surfacesterilised in 3% sodium hypochlorite solution during 20 minutes andwashed in distilled water with 500 μg/ml cefotaxime. The seeds are thentransferred to SH-medium with 50 μg/ml benomyl for germination.Hypocotyls of 4 to 6 days old seedlings are removed, cut into 0.5 cmpieces and are placed on 0.8% agar. An Agrobacterium suspension (approx.108 cells per ml, diluted from an overnight culture transformed with thegene of interest and suitable selection markers) is used for inoculationof the hypocotyl explants. After 3 days at room temperature andlighting, the tissues are transferred to a solid medium (1.6 g/lGelrite) with Murashige and Skoog salts with B5 vitamins (Gamborg etal., Exp. Cell Res. 50:151-158 (1968)), 0.1 mg/l 2,4-D, 0.1 mg/l6-furfurylaminopurine and 750 μg/ml MgCL2, and with 50 to 100 μg/mlcefotaxime and 400-500 μg/ml carbenicillin to kill residual bacteria.Individual cell lines are isolated after two to three months (withsubcultures every four to six weeks) and are further cultivated onselective medium for tissue amplification (30° C., 16 hr photoperiod).Transformed tissues are subsequently further cultivated on non-selectivemedium during 2 to 3 months to give rise to somatic embryos. Healthylooking embryos of at least 4 mm length are transferred to tubes with SHmedium in fine vermiculite, supplemented with 0.1 mg/l indole aceticacid, 6 furfurylaminopurine and gibberellic acid. The embryos arecultivated at 30° C. with a photoperiod of 16 hrs, and plantlets at the2 to 3 leaf stage are transferred to pots with vermiculite andnutrients. The plants are hardened and subsequently moved to thegreenhouse for further cultivation.

Example 10 Phenotypic Evaluation Procedure

10.1 Evaluation Setup

Approximately 35 independent T0 rice transformants were generated. Theprimary transformants were transferred from a tissue culture chamber toa greenhouse for growing and harvest of T1 seed. Six events, of whichthe T1 progeny segregated 3:1 for presence/absence of the transgene,were retained. For each of these events, approximately 10 T1 seedlingscontaining the transgene (hetero- and homo-zygotes) and approximately 10T1 seedlings lacking the transgene (nullizygotes) were selected bymonitoring visual marker expression. The transgenic plants and thecorresponding nullizygotes were grown side-by-side at random positions.Greenhouse conditions were of shorts days (12 hours light), 28° C. inthe light and 22° C. in the dark, and a relative humidity of 70%. Plantsgrown under non-stress conditions were watered at regular intervals toensure that water and nutrients were not limiting and to satisfy plantneeds to complete growth and development.

Four T1 events were further evaluated in the T2 generation following thesame evaluation procedure as for the T1 generation but with moreindividuals per event. From the stage of sowing until the stage ofmaturity the plants were passed several times through a digital imagingcabinet. At each time point digital images (2048×1536 pixels, 16 millioncolours) were taken of each plant from at least 6 different angles.

10.2 Statistical Analysis: F Test

A two factor ANOVA (analysis of variants) was used as a statisticalmodel for the overall evaluation of plant phenotypic characteristics. AnF test was carried out on all the parameters measured of all the plantsof all the events transformed with the gene of the present invention.The F test was carried out to check for an effect of the gene over allthe transformation events and to verify for an overall effect of thegene, also known as a global gene effect. The threshold for significancefor a true global gene effect was set at a 5% probability level for theF test. A significant F test value points to a gene effect, meaning thatit is not only the mere presence or position of the gene that is causingthe differences in phenotype.

Where two experiments with overlapping events were carried out, acombined analysis was performed. This is useful to check consistency ofthe effects over the two experiments, and if this is the case, toaccumulate evidence from both experiments in order to increaseconfidence in the conclusion. The method used was a mixed-model approachthat takes into account the multilevel structure of the data (i.e.experiment-event-segregants). P values were obtained by comparinglikelihood ratio test to chi square distributions.

10.3 Parameters Measured

Biomass-Related Parameter Measurement

From the stage of sowing until the stage of maturity the plants werepassed several times through a digital imaging cabinet. At each timepoint digital images (2048×1536 pixels, 16 million colours) were takenof each plant from at least 6 different angles.

The plant aboveground area (or leafy biomass) was determined by countingthe total number of pixels on the digital images from aboveground plantparts discriminated from the background. This value was averaged for thepictures taken on the same time point from the different angles and wasconverted to a physical surface value expressed in square mm bycalibration. Experiments show that the aboveground plant area measuredthis way correlates with the biomass of plant parts above ground. Theabove ground area is the area measured at the time point at which theplant had reached its maximal leafy biomass. The early vigour is theplant (seedling) aboveground area three weeks post-germination. Increasein root biomass is expressed as an increase in total root biomass(measured as maximum biomass of roots observed during the lifespan of aplant); or as an increase in the root/shoot index (measured as the ratiobetween root mass and shoot mass in the period of active growth of rootand shoot).

Early vigour was determined by counting the total number of pixels fromaboveground plant parts discriminated from the background. This valuewas averaged for the pictures taken on the same time point fromdifferent angles and was converted to a physical surface value expressedin square mm by calibration. The results described below are for plantsthree weeks post-germination.

Seed-Related Parameter Measurements

The mature primary panicles were harvested, counted, bagged,barcode-labelled and then dried for three days in an oven at 37° C. Thepanicles were then threshed and all the seeds were collected andcounted. The filled husks were separated from the empty ones using anair-blowing device. The empty husks were discarded and the remainingfraction was counted again. The filled husks were weighed on ananalytical balance. The number of filled seeds was determined bycounting the number of filled husks that remained after the separationstep. The total seed yield was measured by weighing all filled husksharvested from a plant. Total seed number per plant was measured bycounting the number of husks harvested from a plant. Thousand KernelWeight (TKW) is extrapolated from the number of filled seeds counted andtheir total weight. The Harvest Index (HI) in the present invention isdefined as the ratio between the total seed yield and the above groundarea (mm²), multiplied by a factor 10⁶. The total number of flowers perpanicle as defined in the present invention is the ratio between thetotal number of seeds and the number of mature primary panicles. Theseed fill rate as defined in the present invention is the proportion(expressed as a %) of the number of filled seeds over the total numberof seeds (or florets).

Examples 11 Results of the Phenotypic Evaluation of the TransgenicPlants

1. SGT1 Polypeptides

The results of the evaluation of transgenic rice plants in the T2generation and expressing a nucleic acid comprising the longest OpenReading Frame in SEQ ID NO: 1 under non-stress conditions are presentedbelow.

Parameter % Overall Total weight seeds 10.5 Fill rate 10.6 Harvest index10.0 Number filled seeds 11.3 Number of Flowers per panicle 6.6

For each parameter, the percentage overall difference between transgenicand control plants (corresponding nullizygotes) is shown if valuereaches p<0.05 and above the 5% threshold.

2. CLC-pKG Polypeptides

The results of the evaluation of transgenic rice plants in the T1generation and expressing a nucleic acid comprising the Open ReadingFrame in SEQ ID NO: 53 encoding the polypeptide of SEQ ID NO: 54 undernon-stress conditions are presented below. See previous Examples fordetails on the generations of the transgenic plants.

The results of the evaluation of transgenic rice plants under non-stressconditions are presented below. An increase of at least 5% was observedfor aboveground biomass (AreaMax), plant height (HeightMax), emergencevigour (early vigour; EmerVigor), root biomass (RootMax), total seedyield (totalwgseeds), harvest index (harvestindex), Proportion of thickroots compared to thin roots (RootThickMax), Gravity center of thecanopy of the plants (GravityYMax). The last two parameters areindicative of a change in the architecture of the root system and of thecanopy of the plant, respectively.

TABLE E1 Data summary for transgenic rice plants; for each yield-relatedtrait, the overall percent increase is shown for the T1 generation, foreach parameter the p-value is <0.05. % increase in the transgenic Yieldrelated trait compared to the control plants AreaMax 10.6 EmerVigor 6.0RootMax 11.1 totalwgseeds 17.4 harvestindex 9.3 HeightMax 5.7GravityYMax 7.3 RootThickMax 7.8

3. HD-Hydrolase-Like Polypeptides

The results of the evaluation of transgenic T1 rice plants andexpressing a nucleic acid encoding the polypeptide of SEQ ID NO: 119under non-stress conditions are presented below in Table E2.

TABLE E2 Data summary for transgenic rice plants; for each parameter,the overall percent increase is shown for the confirmation (T1generation), for each parameter the p-value is <0.05. Parameter Overallincrease totalwgseeds 15.4 fillrate 12.7 harvestindex 14.1 flowerperpan9.2 Height 7.0

1. A method for enhancing a yield-related trait in a plant relative to acontrol plant, comprising modulating expression in a plant of a nucleicacid encoding a CLC-pKG polypeptide, wherein said CLC-pKG polypeptidecomprises a Voltage_CLC domain and a CBS domain, and optionally a USPdomain.
 2. The method of claim 1, wherein said CLC-pKG polypeptidecomprises a domain having at least 25% sequence identity to: (i) theVoltage_CLC domain of SEQ ID NO: 54 located between amino acids 77 and422 of SEQ ID NO: 54; (ii) the CBS domain of SEQ ID NO: 54 locatedbetween amino acids 455 to 510 or 516 to 571 of SEQ ID NO: 54; andoptionally (iii) the USP domain of SEQ ID NO: 54 located between aminoacids 597-731 of SEQ ID NO:
 54. 3. The method of claim 1, wherein saidmodulated expression is effected by introducing and expressing in aplant a genetic construct comprising a nucleic acid encoding saidCLC-pKG polypeptide.
 4. The method of claim 1, wherein said nucleic acidencodes any one of the proteins listed in Table A2 or is a portion ofsuch a nucleic acid, or a nucleic acid capable of hybridizing with sucha nucleic acid.
 5. The method of claim 1, wherein said nucleic acidencodes an orthologue or paralogue of any of the proteins given in TableA2.
 6. The method of claim 1, wherein said nucleic acid is selected fromthe group consisting of: (i) a nucleic acid comprising the nucleotidesequence of SEQ ID NO: 53; (ii) a nucleic acid encoding a polypeptidecomprising the amino acid sequence of SEQ ID NO: 54; and (iii) a nucleicacid encoding a polypeptide having at least 80% sequence identity to theamino acid sequence of SEQ ID NO:
 54. 7. The method of claim 1, whereinsaid enhanced yield-related trait comprises increased yield, increasedbiomass, and/or increased seed yield relative to a control plant.
 8. Themethod of claim 1, wherein said enhanced yield-related trait is obtainedunder non-stress conditions or under conditions of drought stress, orsalt stress.
 9. The method of claim 3, wherein said nucleic acid isoperably linked to a constitutive promoter, a RCc3 promoter, or a RCc3promoter from rice.
 10. The method of claim 1, wherein said nucleic acidis of cyanobacterial origin, from Synechosystis species, or fromSynechocystis sp. PCC
 6803. 11. A plant obtained by the method of claim1, or a plant cell, plant part, seed, or progeny thereof, wherein saidplant, or said plant cell, plant part, seed, or progeny thereof,comprises a recombinant nucleic acid encoding said CLC-pKG polypeptide.12. A construct comprising: (i) a nucleic acid encoding a CLC-pKGpolypeptide as defined in claim 1; (ii) one or more heterologous controlsequences capable of driving expression of the nucleic acid of (i); andoptionally (iii) a transcription termination sequence.
 13. The constructof claim 12, wherein one of said control sequences is a constitutivepromoter, a RCc3 promoter, or a RCc3 promoter from rice.
 14. A methodfor making a plant having increased yield, increased biomass, and/orincreased seed yield relative to a control plant, comprisingtransforming the construct of claim 12 into a plant, plant cell or plantpart.
 15. A plant, plant part or plant cell comprising the construct ofclaim
 12. 16. A method for the production of a transgenic plant havingincreased yield, increased biomass, and/or increased seed yield relativeto a control plant, comprising: (i) introducing and expressing in aplant a nucleic acid encoding a CLC-pKG polypeptide as defined in claim1; and (ii) cultivating the plant under conditions promoting plantgrowth and development.
 17. A transgenic plant having increased yield,increased biomass, and/or increased seed yield relative to a controlplant, resulting from modulated expression of a recombinant nucleic acidencoding a CLC-pKG polypeptide as defined in claim 1, or a transgenicplant cell derived from said transgenic plant.
 18. The transgenic plantof claim 17, or a transgenic plant cell derived thereof, wherein saidplant is a crop plant, a monocot or a cereal, or wherein said plant isrice, maize, wheat, barley, millet, rye, triticale, sorghum emmer,spelt, secale, einkorn, teff, milo or oats.
 19. Harvestable parts of thetransgenic plant of claim 17, wherein said harvestable parts comprise arecombinant nucleic acid encoding said CLC-pKG polypeptide.
 20. Productsderived from the transgenic plant of claim 17 and/or from harvestableparts of said plant, wherein said products comprise a recombinantnucleic acid encoding said CLC-pKG polypeptide.